Electronic Submission of a Sequence Listing, a Large Table, or a Computer Program Listing Appendix in Patent Applications

Published date26 May 2021
Citation86 FR 28301
Record Number2021-10421
SectionProposed rules
CourtPatent And Trademark Office
Federal Register, Volume 86 Issue 100 (Wednesday, May 26, 2021)
[Federal Register Volume 86, Number 100 (Wednesday, May 26, 2021)]
                [Proposed Rules]
                [Pages 28301-28323]
                From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
                [FR Doc No: 2021-10421]
                [[Page 28301]]
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                DEPARTMENT OF COMMERCE
                 Patent and Trademark Office
                37 CFR Part 1
                [Docket No. PTO-P-2020-0032]
                RIN 0651-AD48
                Electronic Submission of a Sequence Listing, a Large Table, or a
                Computer Program Listing Appendix in Patent Applications
                AGENCY: United States Patent and Trademark Office, Department of
                Commerce.
                ACTION: Notice of proposed rulemaking.
                -----------------------------------------------------------------------
                SUMMARY: The United States Patent and Trademark Office (USPTO or
                Office) proposes to amend the rules of practice to permit higher-
                capacity physical media to be submitted to the USPTO. Patent
                applications for certain inventions require significant data in
                American Standard Code for Information Interchange (ASCII) text format
                to be submitted to the USPTO in order to determine whether the
                invention described in the patent application is patentable. When
                submission of such data exceeds the USPTO's patent electronic filing
                system capacity, direct submission would not be possible for a large
                data submission in ASCII text format. To that end, the rules of
                practice are proposed to be amended to provide applicants with the
                ability to use physical media larger than compact discs (CDs) for
                submission of an electronic version of amino acid and nucleotide
                sequence information, information compiled in a large table, and
                information relating to a computer program listing. Additionally,
                changes regarding extraction of compressed data files, which had not
                been permitted in the past for certain submissions, would be permitted
                if compliant with the requirements of the proposed rules. Other rules
                relating to certain obsolete and non-secure methods of presenting data
                would be eliminated.
                DATES: Comments must be received by July 26, 2021 to ensure
                consideration.
                ADDRESSES: For reasons of Government efficiency, comments must be
                submitted through the Federal eRulemaking Portal at
                www.regulations.gov. To submit comments via www.regulations.gov, enter
                docket number PTO-P-2020-0032 on the homepage and click ``Search.'' The
                site will provide a search results page listing all documents
                associated with this docket. Find a reference to this document and
                click on the ``Comment Now!'' icon, complete the required fields, and
                enter or attach your comments. Attachments to electronic comments will
                be accepted in ADOBE[supreg] portable document format or MICROSOFT
                WORD[supreg] format. Because comments will be made available for public
                inspection, information that the submitter does not desire to make
                public, such as an address or phone number, should not be included in
                the comments.
                 Visit the Federal eRulemaking Portal website (www.regulations.gov)
                for additional instructions on providing comments via the portal. If
                electronic submission of comments is not feasible due to lack of access
                to a computer and/or the internet, please contact the USPTO using the
                contact information below for special instructions.
                FOR FURTHER INFORMATION CONTACT: Mary C. Till, Senior Legal Advisor,
                Office of Patent Legal Administration, Office of the Deputy
                Commissioner for Patents, by email at [email protected]; or Ali
                Salimi, Senior Legal Advisor, Office of Patent Legal Administration,
                Office of the Deputy Commissioner for Patents, by email at
                [email protected]. Contact via telephone at 571-272-7704 if further
                instruction is needed for the submission of comments.
                SUPPLEMENTARY INFORMATION:
                 Background: In order to permit the submission of large amounts of
                data in patent applications where such a submission exceeds the
                capacity for filing via the USPTO patent electronic filing systems,
                this rulemaking seeks to expand the types of physical media that can be
                used for such a submission. The volume of applications in which such
                large amounts of data may need to be submitted is a small fraction of
                the total number of applications that the USPTO receives every year.
                Expanding the types of physical media that can be used by these
                applicants achieves the intent with minimal changes to the USPTO's
                processing of such large amounts of data.
                 With respect to the submission of data relating to biotechnology
                inventions, the proposed rules would no longer permit an applicant to
                rely on a previously submitted computer readable form (CRF) of required
                sequence information. The proposed rules thus ensure the robustness of
                the data by requiring the applicant to confirm that the data presented
                is the correct information for the examiner to consider during the
                examination process. Since the proposed rules will also permit an ASCII
                plain text file to serve as both the sequence listing itself and the
                CRF of the sequence listing, these changes are expected to have a
                minimal impact on applicants in general.
                 The USPTO encourages applicants to file their patent applications
                via its USPTO patent electronic filing system and imposes a surcharge
                for non-electronic filing of an original patent application (excluding
                reissue, design, plant, and provisional applications), as mandated by
                section 10(h) of Public Law 112-29, September 16, 2011 (Leahy-Smith
                America Invents Act). The USPTO provides information (Legal Framework
                for Patent Electronic System) concerning electronic filing via the
                USPTO patent electronic filing system on its website at www.uspto.gov/patents-application-process/filing-online/legal-framework-efs-web and
                in section 502.05 of the Manual of Patent Examining Procedure (MPEP,
                Ninth Edition, Revision 10.2019). In particular, the USPTO patent
                electronic filing system permits submission of ASCII plain text files
                (.txt) for submission of a ``Sequence Listing,'' a CRF of a ``Sequence
                Listing,'' ``Large Tables,'' and a ``Computer Program Listing
                Appendix.'' Although a USPTO patent electronic filing system submission
                of such ASCII plain text files is preferred, it is possible that the
                system limitations of the USPTO patent electronic filing system may not
                accommodate large ASCII text files. Currently, in those circumstances,
                such text files may be submitted on compact disc under 37 CFR 1.52(e),
                and images of such text files may be submitted in Portable Document
                Format (PDF) via the USPTO patent electronic filing system (except for
                a CRF of a ``Sequence Listing'' or a ``Computer Program Listing
                Appendix'' having over 300 lines--these must be submitted on compact
                disc under 37 CFR 1.52(e)). The proposed changes to the rules of
                practice pertaining to a ``Sequence Listing,'' a CRF of a ``Sequence
                Listing,'' ``Large Tables,'' and a ``Computer Program Listing
                Appendix'' would harmonize the rules for filing such documents in
                electronic form with the requirements and conditions set forth in the
                Legal Framework for Patent Electronic System. The proposed changes do
                not alter the requirements and conditions set forth in the Legal
                Framework for Patent Electronic System.
                 Submission of ASCII plain text files: Currently, electronic
                documents in ASCII file format that are to become part of the permanent
                USPTO records in the file of a patent application, reexamination, or
                supplemental examination proceeding that exceed the USPTO patent
                electronic filing system limits may be submitted on a compact disc. Due
                to the limited storage capacity
                [[Page 28302]]
                of compact discs, the USPTO is proposing revisions to permit use of
                Digital Video Disc-Recordable (DVD-R or DVD+R). These higher-capacity
                read-only optical discs, on which data is permanently recorded and
                cannot be changed or erased, significantly reduce the number of
                physical media required to accommodate large files.
                 In the case of a ``Sequence Listing,'' MPEP section 2422.03
                indicates that if a new application is filed via the USPTO patent
                electronic filing system with an ASCII plain text file of a ``Sequence
                Listing'' that complies with the requirements of 37 CFR 1.824(a)(2)
                through (6) and (b), and the applicant has not filed a ``Sequence
                Listing'' in a PDF image file, the text file will serve as both the
                paper copy required by 37 CFR 1.821(c) and the CRF required by 37 CFR
                1.821(e). This concept is expressly incorporated into these proposed
                changes to the rules of practice. The current size limitation for an
                ASCII plain text file of a ``Sequence Listing'' submitted via the USPTO
                patent electronic filing system is 100 megabytes (MB). Thus, if an
                applicant files an ASCII plain text file of a ``Sequence Listing'' that
                is 100 MB or less, that ASCII plain text file serves as both the
                ``Sequence Listing'' under 37 CFR 1.821(c) and the CRF of the
                ``Sequence Listing'' under 37 CFR 1.821(e). With respect to ``Large
                Tables'' and a ``Computer Program Listing Appendix,'' if ASCII plain
                text files are filed through the USPTO patent electronic filing system,
                then no separate submission of disc copies of ASCII plain text files
                are needed. However, the current system limit of ASCII plain text file
                submissions of ``Large Tables'' and a ``Computer Program Listing
                Appendix'' is 25 MB per submission. This limit, however, may not
                prevent an entirely electronic submission. According to the Legal
                Framework for Patent Electronic System, cited supra, a user may be able
                to break up a ``Computer Program Listing Appendix'' or ``Large Tables''
                file that is larger than 25 MB into multiple files that are no larger
                than 25 MB each and submit those smaller files via the USPTO patent
                electronic filing system. If the user chooses to break up a large
                ``Computer Program Listing Appendix'' or ``Large Tables'' file so it
                may be submitted electronically, the file names must indicate their
                order (e.g., ``1 of X,'' ``2 of X''). Files above the 25 MB limit for
                ``Large Tables'' and a ``Computer Program Listing Appendix'' (unless
                capable of being divided) and above 100 MB for a ``Sequence Listing''
                will have to be submitted on read-only optical discs. Submission of a
                ``Sequence Listing'' as an ASCII text file, if it exceeds 100 MB,
                cannot be divided like a submission of a ``Large Table'' or a
                ``Computer Program Listing Appendix.'' Thus, any ``Sequence Listing''
                greater than 100 MB must be submitted on read-only optical discs.
                Currently, such files cannot be compressed; this can necessitate the
                use of multiple CD-ROMs or CD-Rs. These proposed changes to the rules
                of practice will permit higher-capacity media as well as non-self-
                extracting file compression. By permitting file compression, material
                submitted on a read-only optical disc will be capable of fitting on a
                single disc with the data integrity remaining intact.
                 The current rules of practice (37 CFR 1.52(e), 1.96(c), and 1.824)
                recite the use of certain obsolete computer and operating system
                formats. Updated computer and operating system formats are proposed to
                be added, and reference to obsolete media will be eliminated. Proposed
                changes to 37 CFR 1.58 will recite the updated computer and operating
                system compatibilities.
                 When a patent application relies on subject matter from an ASCII
                plain text file submitted on physical media or via the USPTO patent
                electronic filing system, currently, the patent specification must
                contain an incorporation by reference statement pursuant to 37 CFR
                1.77(b)(5) or the Legal Framework for Patent Electronic System. The
                rules relating to the arrangement of the specification are proposed to
                be amended to clarify the required incorporation by reference
                statement. The granted patent or pre-grant publication of an
                application that includes an ASCII plain text file, whether submitted
                on optical read-only discs or via the USPTO patent electronic filing
                system, does not include the actual contents of the ASCII plain text
                file in the printed document. The incorporation by reference is
                necessary to treat the material in the ASCII file as part of the patent
                or publication and to alert the public that the granted patent or the
                pre-grant publication includes additional material that constitutes
                part of the patent or publication. Although the current rules and
                proposed changes to the rules of practice permit a cross-reference to
                related applications to be included in the specification, in accordance
                with 37 CFR 1.76, it should be noted that the USPTO does not recognize
                a benefit or priority claim presented only in the specification for
                patent applications filed on or after September 16, 2012. For these
                applications or patents issued from such applications, a benefit claim
                (37 CFR 1.78) or priority claim (37 CFR 1.55) must be presented on an
                Application Data Sheet for an original application in order to be
                recognized by the USPTO.
                 Sequence Listings: Any patent application that contains unbranched
                nucleotide sequences with 10 or more nucleotide bases or unbranched,
                non-D amino acid sequences with 4 or more amino acids, provided that
                there are at least 10 ``specifically defined'' nucleotides or 4
                ``specifically defined'' amino acids, must contain a ``Sequence
                Listing'' and a CRF of the ``Sequence Listing.'' Under the current
                rules, a ``Sequence Listing'' exceeding the USPTO patent electronic
                filing system submission limit must be submitted with a total of three
                disc copies to the USPTO to comply with the ``Sequence Listing''
                regulation requirements. The three disc copies are (1) a first disc
                copy of ASCII plain text file on a compact disc to comply with 37 CFR
                1.821(c), (2) a second identical disc copy of the ASCII plain text file
                on compact disc to comply with the duplicate submission requirement in
                37 CFR 1.52(e)(4) when submitting the 37 CFR 1.821(c) sequence listing,
                and (3) a CRF copy of the ASCII plain text file on compact disc,
                identical to the 37 CFR 1.821(c) submission. The proposed rule changes
                would permit that a single read-only optical disc copy of a ``Sequence
                Listing'' as an ASCII plain text file could be submitted, and that such
                submission would comply with both the listing requirement (37 CFR
                1.821(c)) and the CRF requirement (37 CFR 1.821(e)). For submission via
                the USPTO patent electronic filing system, the ASCII plain text file,
                not the PDF version, would serve to comply with both 37 CFR 1.821(c)
                and 1.821(e). The following table summarizes the mechanics of
                submitting a ``Sequence Listing'' under the proposed changes to the
                rules of practice in applications, except for international
                applications during the international stage, based on the current USPTO
                patent electronic filing system limit of 100 MB for an ASCII plain text
                file and a system limit of 25 MB for PDF files.
                [[Page 28303]]
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                 Surcharge under 37
                 CFR 1.21(o) for
                 Preferred Acceptable Specification submission of a
                 Size of ``Sequence Listing'' submission submission statement ``Sequence
                 requirements Listing'' in
                 electronic form
                ----------------------------------------------------------------------------------------------------------------
                100 MB or less.................. ASCII plain text The ``Sequence Incorporation by None.
                 file submitted Listing'' in reference of the
                 via the USPTO physical paper ASCII text file
                 patent electronic copies or into the
                 filing system, submitted via the specification
                 complies with USPTO patent (see MPEP 502.05).
                 both 37 CFR electronic filing
                 1.821(c) and system as a PDF
                 1.821(e), no image file and a
                 separate CRF CRF on a read-
                 needed. only optical disc
                 along with a
                 statement that
                 the CRF and the
                 physical paper/
                 PDF image file
                 submission are
                 the same.
                101 MB to 299 MB................ ASCII plain text The ``Sequence Incorporation by None.
                 file submitted on Listing'' in reference of the
                 a read-only physical paper ASCII text file
                 optical disc in a copies and a CRF into the
                 single copy, the on a read-only specification (37
                 single copy optical disc CFR 1.52(e)(8)).
                 complies with along with a
                 both 37 CFR statement that
                 1.821(c) and the CRF and the
                 1.821(e), no physical paper
                 separate CRF submission are
                 needed. the same.
                300 MB to 799 MB................ ASCII plain text The ``Sequence Incorporation by 37 CFR 1.21(o)(1):
                 file submitted on Listing'' in reference of the Currently $1,000
                 a read-only physical paper ASCII text file for an
                 optical disc in a copies and a CRF into the undiscounted
                 single copy, the on a read-only specification (37 entity, $500 for
                 single copy optical disc CFR 1.52(e)(8)). a small entity,
                 complies with along with and $250 for a
                 both 37 CFR statement that micro entity.
                 1.821(c) and the CRF and the
                 1.821(e), no physical paper
                 separate CRF submission are
                 needed. the same.
                800 MB or above................. ASCII plain text The ``Sequence Incorporation by 37 CFR 1.21(o)(2):
                 file submitted on Listing'' in reference of the Currently $10,000
                 a read-only physical paper ASCII text file for an
                 optical disc in a copies and a CRF into the undiscounted
                 single copy, the on a read-only specification (37 entity, $5,000
                 single copy optical disc CFR 1.52(e)(8) as for a small
                 complies with along with a added in these entity, and
                 both 37 CFR statement that proposed rules). $2,500 for a
                 1.821(c) and the CRF and the micro entity.
                 1.821(e), no physical paper
                 separate CRF submission are
                 needed. Should the same.
                 more than one
                 disc be needed,
                 then only a
                 single copy of
                 the additional
                 disc(s) would be
                 needed, no
                 additional CRF
                 needed since the
                 read-only optical
                 discs (if
                 multiple are
                 needed) need NOT
                 be submitted in
                 duplicate.
                ----------------------------------------------------------------------------------------------------------------
                 The current rules of practice relating to form, content, and
                submission requirements of ``Sequence Listings'' comply with World
                Intellectual Property Organization (WIPO) Standard ST.25. In this
                document, the proposed rule changes and modifications also conform to
                WIPO Standard ST.25.
                 To simplify and streamline the processing of patent applications
                with sequences of amino acids and nucleotides as defined in 37 CFR
                1.821(a), submission of a ``Sequence Listing'' in ASCII plain text file
                format, either directly via the USPTO patent electronic filing system
                or on a read-only optical disc, will be sufficient to comply with the
                listing requirement and the CRF requirement (37 CFR 1.821(c) and
                1.821(e)). That is, if a ``Sequence Listing'' in ASCII plain text file
                format is filed either directly via the USPTO patent electronic filing
                system or on a read-only optical disc, then no additional CRF copy will
                be needed. In such a situation, an incorporation by reference statement
                in the specification, in accordance with 37 CFR 1.77(b)(5), would still
                be required, except such a statement will not be required in an
                international application during the international stage. As with the
                current rules, the proposed changes continue to permit submission of a
                ``Sequence Listing'' on physical sheets of paper or as a PDF image
                file. Furthermore, like the current rules, the proposed rules will
                require payment of the application size fee (37 CFR 1.16(s)) for
                physical sheets of paper of a ``Sequence Listing'' or a PDF of a
                ``Sequence Listing'' that results in an application size that exceeds
                100 sheets of paper. Submission of the ``Sequence Listing'' as a PDF or
                on physical sheets of paper would still require a separate CRF of the
                ``Sequence Listing.'' Similarly, should the ASCII plain text file of
                the ``Sequence Listing'' exceed the system limits of the USPTO patent
                electronic filing system (currently at 100 MB), then a single copy of
                an ASCII plain text file of the ``Sequence Listing'' submitted on a
                read-only optical disc would not require a separate electronic copy of
                a CRF of the ``Sequence Listing.'' In circumstances in which a separate
                CRF is filed, the statement, in accordance with 37 CFR
                1.821(e)(2)(iii), that the CRF is identical to either the PDF or the
                physical paper version of the ``Sequence Listing'' is required.
                 The proposed rule changes will no longer permit the transfer of a
                CRF from a parent or related application to the newly filed original
                application. In light of the availability to download a ``Sequence
                Listing'' from granted U.S. patents and U.S. patent application
                publications via Public PAIR in the Supplemental Content tab, there is
                no longer a need for a CRF transfer. Such electronic copies of a
                ``Sequence Listing'' may also be available on another intellectual
                property office's website or on the WIPO--PATENTSCOPE website. In the
                extremely rare circumstance in which the ``Sequence Listing'' exceeds
                the download capability (currently 650 MB), then a request for the
                content of a granted U.S. patent or U.S. patent application publication
                (including the ``Sequence Listing'' submitted on disc) can be made to
                the Patent and Trademark Copy Fulfillment Branch. Therefore, these
                proposed changes to the rules of practice will eliminate the practice
                of CRF transfers.
                 WIPO Standard ST.26 is expected to take effect on January 1, 2022,
                and will replace WIPO Standard ST.25. WIPO Standard ST.26 will require
                that a
                [[Page 28304]]
                ``Sequence Listing'' must be presented as a single file in eXtensible
                Markup Language (XML). As a result, in an original application filed on
                or after January 1, 2022, the ``Sequence Listing'' part will not be
                accepted on physical sheets of paper or as a PDF image file. Therefore,
                to prepare for the changes under WIPO Standard ST.26, the USPTO is
                proposing to revise the rules of practice to facilitate ``Sequence
                Listing'' submissions by requiring a single ASCII plain text file
                submission that would both meet the ``Sequence Listing'' requirement
                and serve as the CRF of the ``Sequence Listing.'' That is, under these
                proposed rule changes, a single ASCII plain text file submission of a
                ``Sequence Listing'' would comply with both 37 CFR 1.821(c) and (e).
                 Currently, 37 CFR 1.821(a) incorporates by reference six tables
                from Appendix 2 of WIPO Standard ST.25 that provide the nucleotide and
                amino acid symbols and feature tables. For convenience, a further
                proposed modification of the ``Sequence Listing'' rules involves adding
                these tables as Appendices A-F of Subpart G of Part 1 (explicitly
                incorporating the text of the WIPO tables into the CFR). Currently, 37
                CFR 1.823(b) includes a table containing all numeric identifiers. To
                improve the readability of the regulations, this table is proposed to
                be moved to Appendix G.
                 Updates to amendment practice for ``Large Tables,'' a ``Computer
                Program Listing Appendix,'' and ``Sequence Listings'': In general, the
                manner of making amendments in applications requires that the text of
                any added subject matter must be shown by underlining the added text
                and that the text of any deleted matter must be shown by strike-
                through. However, computer listings (37 CFR 1.96) and ``Sequence
                Listings'' (37 CFR 1.825) are currently exempted from these general
                requirements (37 CFR 1.121(b)). These proposed changes to the rules of
                practice will require a description of the amendments made in ``Large
                Tables,'' a ``Computer Program Listing Appendix,'' and ``Sequence
                Listings'' to more easily and accurately identify any changes made to
                the information contained in such submissions (37 CFR 1.121(b)(6)).
                 This proposed rule includes requirements for amendments to an ASCII
                plain text file containing ``Large Tables'' (37 CFR 1.58(g)) or a
                ``Computer Program Listing Appendix'' (37 CFR 1.96(c)(5)(i)) that are
                accomplished by a replacement of an ASCII plain text file. Providing a
                replacement may be required if, for example, the information on the
                disc is corrupted. A replacement ASCII plain text file must be
                submitted, either via the USPTO patent electronic filing system or on a
                read-only optical disc, together with an incorporation by reference of
                the material in the replacement ASCII plain text file in a separate
                paragraph of the specification; a statement that identifies the
                location of all deletions, replacements, or additions to the ASCII
                plain text file; and a statement that the replacement ASCII plain text
                file contains no new matter.
                Discussion of Specific Rules
                 Section 1.52: The heading of Sec. 1.52 is proposed to read:
                Language, paper, writing, margins, read-only optical disc
                specifications.
                 Section 1.52(e) is proposed to be amended to reference electronic
                documents ``submitted on a read-only optical disc,'' with additional
                conforming changes made throughout. Currently, Sec. 1.52(e) references
                ``electronic documents'' that are to become part of the USPTO records
                in patent applications, reexaminations, and supplemental examination
                proceedings. Since Sec. 1.52(e) only governs electronic documents
                submitted on discs, in particular as proposed, read-only optical discs,
                the heading is more specific to the types of electronic documents
                covered by the regulation.
                 Section 1.52(e)(1) is proposed to be updated to specifically refer
                to a ``Computer Program Listing Appendix,'' as provided for in Sec.
                1.96(c), and to require that the ``Sequence Listing'' on a read-only
                optical disc submitted under Sec. 1.821(c) must be in compliance with
                Sec. 1.824. Section 1.52(e)(1) is proposed to be revised to indicate
                that ``Large Tables,'' as described in the proposed changes to Sec.
                1.58(c), may be submitted on a read-only optical disc to become part of
                the permanent USPTO record.
                 Section 1.52(e)(2) is proposed to be revised to replace ``compact''
                with ``read-only optical'' and to incorporate conformity to the
                International Organization for Standardization (ISO) 9660 standard,
                which was previously located in Sec. 1.52(e)(3). Additionally, Sec.
                1.52(e)(2) maintains the availability of CD-ROM and CD-R as options for
                physical media (Sec. 1.52(e)(2)(i)) but also expands the types of
                media options to include Digital Video Disc-Recordable (DVD-R or DVD+R)
                (Sec. 1.52(e)(2)(ii)).
                 Section 1.52(e)(3) is proposed to be reorganized for improved
                readability. The computer compatibility (Sec. 1.52(e)(3)(i)) and
                operating system compatibility (Sec. 1.52(e)(3)(ii)) are expressly
                provided. Furthermore, the proposed changes to the rules of practice
                indicate the use of ASCII plain text is required when submitting files
                on physical media (Sec. 1.52(e)(3)(iii)). The proposed changes would
                permit file compression for ASCII plain text files, which must be done
                in accordance with Sec. Sec. 1.58, 1.96, and 1.824, as applicable
                (Sec. 1.52(e)(3)(iii)).
                 Section 1.52(e)(4) is proposed to be revised to eliminate its
                requirements for a duplicate copy and accompanying statement that the
                two discs are identical. References to ``Copy 1'' and ``Copy 2'' are
                deleted, and references to ``compact disc'' are updated to ``read-only
                optical disc.'' However, duplicate copies of read-only optical discs
                for ``Large Tables'' or a ``Computer Program Listing Appendix'' will
                still be required, and Sec. Sec. 1.58 and 1.96 are proposed to be
                amended to provide for such duplicate copies. Duplicate copies for
                ``Large Tables'' and a ``Computer Program Listing Appendix'' would
                still be required to be submitted since the Office of Patent
                Application Processing (OPAP) keeps a first copy for record retention
                purposes and a second copy in an artifact folder for use by the
                examiner during the patent examination process. A ``Sequence Listing,''
                however, is not processed in the same manner. Accordingly, only a
                single copy of a read-only optical disc containing the ``Sequence
                Listing'' in ASCII plain text is needed, as such copy will serve as
                both the listing as required by 37 CFR 1.821(c) and the CRF copy as
                required by 37 CFR 1.821(e). Section 1.52(e)(4) is also proposed to
                require that the read-only optical discs are enclosed in a hard case
                within an unsealed, padded, and protective mailing envelope and that
                such submission is accompanied by a transmittal letter. The information
                regarding the read-only optical disc to be included in the transmittal
                letter is expressly enumerated in items (i)-(vi) of this rule.
                 Section 1.52(e)(5) is proposed to be revised to enumerate the
                labeling requirements of the read-only optical disc that had previously
                been enumerated in Sec. 1.52(e)(6). The incorporation by reference
                found in the current Sec. 1.52(e)(5) is deleted and moved to Sec.
                1.52(e)(8).
                 Section 1.52(e)(6) is proposed to be revised to state that the
                read-only optical discs may not be retained as part of the patent
                application file and will not be returned to the applicant. The current
                USPTO processing of compact discs would equally apply to read-only
                optical discs. For ``Large Tables'' or a ``Computer Program Listing
                Appendix,'' the process involves the OPAP receiving the read-only
                optical discs, creating an artifact sheet for inclusion in the Image
                File Wrapper, and reviewing the ASCII plain text file. Under the
                current rules, a first copy of the read-only optical disc
                [[Page 28305]]
                is kept for record retention purposes, and a second copy is maintained
                in an artifact folder for use by the examiner during the patent
                examination process. For a ``Sequence Listing,'' the proposal would
                require the submission of a single read-only optical disc. Once the
                ``Sequence Listing'' is loaded into the USPTO's Supplemental Complex
                Repository for Examiners (SCORE) system, the physical media may be
                retained by the Patent Legal Research Center. A ``Sequence Listing''
                from granted U.S. patents and U.S. patent application publications is
                available via Public PAIR in the Supplemental Content tab. Such
                electronic copies of a ``Sequence Listing'' may also be available on
                another intellectual property office's website, or on the WIPO--
                PATENTSCOPE website. In the extremely rare circumstance in which the
                ``Sequence Listing'' exceeds the download capability (currently 650
                MB), then a request for the content of a granted U.S. Patent or U.S.
                patent application publication (including the ``Sequence Listing''
                submitted on disc) can be made to the Patent and Trademark Copy
                Fulfillment Branch.
                 Section 1.52(e)(7) is proposed to be revised to state that any
                amendment to the information on a read-only optical disc must be made
                in accordance with specified provisions, specifically, in compliance
                with Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a
                ``Computer Program Listing Appendix,'' and Sec. 1.825(b) for a
                ``Sequence Listing'' or a CRF of a ``Sequence Listing.''
                 Section 1.52(e)(8) is proposed to be added to state that the
                specification must contain an incorporation by reference (Sec.
                1.77(b)(5)) of the material contained on each read-only optical disc in
                a separate paragraph, except for an international application in the
                international stage. Additionally, the USPTO may require the applicant
                to amend the specification to include the material incorporated by
                reference.
                 Section 1.52(e)(9) is proposed to be added to indicate that should
                a file be unreadable, then the USPTO will treat the submission as not
                ever having been submitted. A file is unreadable if, for example, it is
                of a format that does not comply with the requirements of Sec.
                1.52(e)(2), it is corrupted, or it is written onto a defective read-
                only optical disc. In such a case, OPAP will issue a notice indicating
                that the file is unreadable, and a replacement will be required.
                 Section 1.52(f) is proposed to be amended to include the subtitle
                ``Determining application size fees for applications containing
                electronic documents submitted on a read-only optical disc or via the
                USPTO patent electronic filing system.''
                 Section 1.52(f)(1) is proposed to be amended to clarify the
                determination of application size fees for application components
                submitted on a read-only optical disc in compliance with Sec. 1.52(e),
                where an electronic form of any ``Sequence Listing,'' in compliance
                with either Sec. 1.821(c) or (e), and any ``Computer Program Listing
                Appendix,'' in compliance with Sec. 1.96(c), are specifically excluded
                from the application size fee determination. As stated in 35 U.S.C.
                41(a)(1)(G), ``any sequence listing'' or a ``computer program listing''
                submitted in electronic form is expressly excluded from any application
                size fee calculation. A ``Computer Program Listing Appendix'' is
                considered a ``computer program listing.''
                 Section 1.52(f)(2) is proposed to be amended to clarify the
                determination of application size fees for applications submitted in
                whole or in part via the USPTO patent electronic filing system and also
                to clarify that any electronic form of a ``Sequence Listing,'' in
                compliance with either Sec. 1.821(c) or (e), and any ``Computer
                Program Listing Appendix,'' in compliance with Sec. 1.96(c), are
                specifically excluded from the application size fee determination. As
                stated in 35 U.S.C. 41(a)(1)(G), ``any sequence listing'' or a
                ``computer program listing'' submitted in electronic form is expressly
                excluded from any application size fee calculation. A ``Computer
                Program Listing Appendix'' is considered a ``computer program
                listing.''
                 Section 1.52(f)(3) is proposed to be added to provide a surcharge
                for submission of a ``Sequence Listing'' in electronic form in an
                application under 35 U.S.C. 111 or 371 that is 300 MB or larger in
                size. The lengthy ``Sequence Listing'' surcharge is set forth in Sec.
                1.21(o). This means that a ``Sequence Listing'' submitted in electronic
                form on read-only optical discs in compliance with either Sec. Sec.
                1.821(c) either/or 1.821(e) that is 300 MB or larger in size will incur
                a surcharge under Sec. 1.21(o). When the electronic form of the
                ``Sequence Listing'' is between 300 MB and 800 MB, a surcharge under
                Sec. 1.21(o)(1) will be required. If the electronic form of the
                ``Sequence Listing'' exceeds 800 MB, then a surcharge under Sec.
                1.21(o)(2) will be imposed.
                 Section 1.58: Section 1.58(b) is proposed to delete references to
                Sec. Sec. 1.96(c) and 1.821(c) regarding tables submitted in
                electronic form and to set forth format requirements, from former Sec.
                1.58(c), that apply generally to chemical and mathematical formulas and
                tables.
                 Section 1.58(c) is proposed to be rewritten to define ``Large
                Tables'' that may be submitted in electronic form in ASCII plain text
                via the USPTO patent electronic filing system or on a read-only optical
                disc, in compliance with Sec. 1.52(e), excluding an international
                application during the international stage. Additionally, the current
                USPTO processing of ``Large Tables'' submitted on a read-only optical
                disc involves a first copy, for record retention purposes, and a second
                copy, for use during the examination process.
                 Section 1.58(d) is proposed to be added to list the format
                requirements of ``Large Tables'' submitted in electronic form in ASCII
                plain text. The format requirements address the spatial relationship of
                table elements, computer compatibility, operating system compatibility,
                the use of ASCII plain text, the naming conventions for the .txt file,
                and an incorporation by reference statement to be included in the
                specification, as per Sec. 1.77(b)(5).
                 Section 1.58(e) is proposed to be added to state that ``Large
                Tables'' submitted via the USPTO patent electronic filing system must
                not exceed 25 MB, and file compression is not permitted. It is noted
                that when submitting via the USPTO patent electronic filing system, it
                is possible to submit multiple files that are 25 MB or less in size, as
                per the Legal Framework for Patent Electronic System cited supra.
                 Section 1.58(f) is proposed to be added to specify the technical
                requirements for ``Large Tables'' submitted on read-only optical discs
                in compliance with Sec. 1.52(e) and that compression is permitted.
                Section 1.58(f) also specifies the permitted manner of file
                compression.
                 Section 1.58(g) is proposed to be added to provide the procedure
                that would be applicable should an amendment of one or more ``Large
                Tables'' be required. If an amendment is required to be made to a
                ``Large Table,'' then a replacement submission via the USPTO patent
                electronic filing system or on duplicate read-only optical discs would
                be necessary. An updated incorporation by reference statement would be
                required along with the necessary statement regarding any deletions,
                replacements or addition to the ASCII plain text file and a statement
                that the replacement ASCII plain text file contains no new matter.
                 Section 1.58(h) is proposed to be added to specify that should
                ``Large Tables'' be submitted as an ASCII plain text file on the
                application filing date,
                [[Page 28306]]
                but no incorporation by reference of the material contained therein has
                been made, an amendment containing a separate paragraph incorporating
                by reference the material contained in the ASCII plain text file, as
                per Sec. 1.77(b)(5), will be required.
                 Section 1.58(i) is proposed to be added to require that any read-
                only optical disc for a ``Large Table'' be submitted in duplicate.
                Section 1.58(i) sets forth the criteria for labeling and necessary
                statements as to the identity of the read-only optical discs. This
                section indicates how the USPTO will treat the submission of the two
                read-only optical discs that are not identical to each other. Duplicate
                copies for ``Large Tables'' are required to be submitted since the OPAP
                keeps a first copy for record retention purposes and a second copy in
                an artifact folder for use by the examiner during the patent
                examination process.
                 Section 1.58(j) is proposed to be added to require that any
                amendment to the information on a read-only optical disc must be by way
                of a replacement read-only optical disc, in compliance with Sec.
                1.58(g), where the replacement read-only optical disc and copy must be
                labeled ``COPY 1 REPLACEMENT MM/DD/YYYY'' (with the month, day, and
                year of creation indicated) and ``COPY 2 REPLACEMENT MM/DD/YYYY,''
                respectively. This section indicates how the USPTO will treat the
                submission of the two replacement read-only optical discs that are not
                identical to each other.
                 Section 1.71: Section 1.71(f) is proposed to be revised to clarify
                that a ``Sequence Listing,'' if required or submitted under Sec.
                1.821(c), should be submitted on a separate sheet. This is directed to
                those submissions of the ``Sequence Listing'' submitted on physical
                sheets of paper or submitted as a PDF image file via the USPTO patent
                electronic filing system. In such cases where there is a separate
                ``Sequence Listing'' and a separate CRF of the ``Sequence Listing,''
                the ``Sequence Listing'' must be on a separate sheet(s).
                 Section 1.77: Section 1.77(b)(5) is proposed to be revised to
                clarify when an incorporation by reference is needed. The proposed rule
                change provides for incorporation by reference of ASCII plain text
                files submitted via the USPTO patent electronic filing system or on one
                or more read-only optical discs for a ``Computer Program Listing
                Appendix,'' a ``Sequence Listing,'' or ``Large Tables,'' as provided
                for in Sec. Sec. 1.96(c), 1.821(c), or 1.58(c), respectively. The
                proposed incorporation by reference statement would identify the names
                of each ASCII plain text file and specify, if applicable, the files
                contained on each of the read-only optical discs, their dates of
                creation, and the sizes of each ASCII plain text file in bytes.
                 Section 1.77(b)(13) is proposed to be revised to clarify that the
                ``Sequence Listing'' required by Sec. 1.821(c), submitted on physical
                sheets of paper or as a PDF image file of the ``Sequence Listing,''
                should follow the other sections of the specification.
                 Section 1.96: Section 1.96(a) is proposed to be revised to replace
                ``printout'' with ``document.''
                 Section 1.96(c) is proposed to be revised to set forth the
                requirements that apply to any ``Computer Program Listing Appendix''
                that will not be part of the printed patent specification. The appendix
                must be submitted as an electronic document in ASCII plain text,
                whether submitted via the USPTO patent electronic filing system or on a
                read-only optical disc, in compliance with Sec. 1.52(e). Proposed
                requirements for the ``Computer Program Listing Appendix'' include that
                it must be incorporated by reference in the specification, as set forth
                in Sec. 1.77(b)(5), and have certain computer compatibilities (Sec.
                1.96(c)(1)), naming convention adherences (Sec. 1.96(c)(2)), and size
                limitations (Sec. 1.96(c)(3)).
                 Section 1.96(c)(4) is proposed to be added to state requirements
                (i) through (vi) where the ``Computer Program Listing Appendix'' is
                submitted on a read-only optical disc, in compliance with Sec.
                1.52(e).
                 Section 1.96(c)(5) is proposed to be added to state requirements
                (i) through (iv) for amendments to delete, replace, or add to the
                information of a ``Computer Program Listing Appendix'' submitted in
                electronic form in ASCII plain text.
                 Section 1.96(c)(6) is proposed to be added to indicate that should
                a ``Computer Program Listing Appendix'' be present on the filing date
                of the application without an express incorporation by reference in the
                specification relating to the material contained in the ASCII plain
                text file, in accordance with Sec. 1.77(b)(5), then an amendment to
                include such a paragraph in the specification will be required.
                 Section 1.96(c)(7) is proposed to be added to indicate that a
                submission of a ``Computer Program Listing Appendix'' on a read-only
                optical disc must be completed in duplicate, since the processing by
                the USPTO of a ``Computer Program Listing Appendix'' submitted on a
                read-only optical disc involves keeping a first copy for record
                retention purposes and using a second copy during the examination
                process. The new section sets forth the criteria for labeling and
                necessary statements as to the identity of the read-only optical discs.
                This proposed section indicates how the USPTO will treat the submission
                of the two read-only optical discs should they not be identical.
                 Section 1.121: Section 1.121(b) is proposed to be revised, and
                Sec. 1.121(b)(6) is proposed to be added, to clarify that ``Large
                Tables'' in accordance with Sec. 1.58(c), a ``Computer Program Listing
                Appendix'' in accordance with Sec. 1.96(c)(5) and (7), and a
                ``Sequence Listing'' or CRF in accordance with Sec. 1.825 must be
                amended in accordance with Sec. 1.58(g), Sec. 1.96(c)(5), and Sec.
                1.825, respectively.
                 Section 1.173: The heading of Sec. 1.173(b)(1) is proposed to be
                revised to reflect that, in a reissue application, changes to the
                claims, ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program Listing
                Appendix'' (Sec. 1.96(c)), or a ``Sequence Listing'' (Sec. 1.821(c))
                are made in a different manner from changes to other parts of the
                specification.
                 The manner of making changes to the specification, other than to
                the claims, set forth in current Sec. 1.173(b)(1) is proposed to be
                moved to new Sec. 1.173(b)(1)(i). New Sec. 1.173(b)(1)(i) specifies
                that it does not apply to changes to ``Large Tables'' (Sec. 1.58(c)),
                a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), or a
                ``Sequence Listing'' (Sec. 1.821(c)), in addition to not applying to
                changes to the claims. Additionally, the language from current Sec.
                1.173(b)(1) stating that the paragraph is not applicable to discs is
                proposed to not be included in new Sec. 1.173(b)(1)(i).
                 Section Sec. 1.173(b)(1)(ii) is proposed to be added to specify
                that changes to ``Large Tables,'' a ``Computer Program Listing
                Appendix,'' or a ``Sequence Listing'' must be made in accordance with
                Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer
                Program Listing Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
                 Section 1.173(d) is proposed to be revised to exclude changes to
                ``Large Tables,'' a ``Computer Program Listing Appendix,'' or a
                ``Sequence Listing'' from the changes that must be shown by markings in
                a reissue application.
                 Section Sec. 1.173(d)(2) is proposed to be revised to delete the
                following: ``except for amendments submitted on compact discs
                (Sec. Sec. 1.96 and 1.821(c)). Matter added by reissue on compact
                discs must be preceded with `' and end with `' to properly
                identify the material being added.''
                 Section 1.530: The heading of Sec. 1.530(d)(1) is proposed to be
                revised to reflect that, in a reexamination proceeding, changes to the
                claims, ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program Listing
                Appendix'' (Sec. 1.96(c)),
                [[Page 28307]]
                and a ``Sequence Listing'' (Sec. 1.821(c)) are made in a different
                manner from changes to the other parts of the specification.
                 The manner of making changes to the specification, other than to
                the claims, set forth in current Sec. 1.530(d)(1) is proposed to be
                moved to new Sec. 1.530(d)(1)(i). New Sec. 1.530(d)(1)(i) specifies
                that it does not apply to changes to ``Large Tables'' (Sec. 1.58(c)),
                a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), and a
                ``Sequence Listing'' (Sec. 1.821(c)), in addition to not applying to
                changes to the claims.
                 Section 1.530(d)(1)(ii) is proposed to be added to specify that
                changes to ``Large Tables,'' a ``Computer Program Listing Appendix,''
                or a ``Sequence Listing'' must be made in accordance with Sec. 1.58(g)
                for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer Program Listing
                Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
                 Section 1.821: Section 1.821(a) is proposed to be revised to remove
                all prior references to WIPO Standard ST.25 (1998) and instead cross-
                reference new Appendices A through F to part 1 of 37 CFR, subpart G,
                which would contain the updated 2009 version of the tables from WIPO
                Standard ST.25.
                 Section 1.821(c) is proposed to be revised to delete references to
                a paper or compact disc copy (Sec. 1.52(e)), delete discussion of
                sequence identifiers, and indicate that the criteria for submission of
                a ``Sequence Listing,'' except for national stage entry under Sec.
                1.495(b)(1), is set forth in newly proposed Sec. 1.821(c)(1)-(3).
                Information about sequence identifiers has been moved to Sec.
                1.823(a).
                 Section 1.821(c)(1) is proposed to be added to require that the
                ``Sequence Listing'' can be submitted as an ASCII plain text file via
                the USPTO patent electronic filing system or on a read-only optical
                disc copy, where the form and format of the ``Sequence Listing''
                conforms to Sec. 1.824 and an incorporation by reference statement as
                required by Sec. 1.52(e) is provided. Section 1.821(c)(2) is proposed
                to be added to permit submission of a ``Sequence Listing'' as a PDF
                file via the USPTO patent electronic filing system. Section 1.821(c)(3)
                is proposed to be added to permit the submission of a ``Sequence
                Listing'' on physical sheets of paper.
                 Section 1.821(d) is proposed to be revised to add that where a
                sequence is presented in a drawing, reference must be made to the
                sequence by use of a sequence identifier, either in the drawing or in
                the Brief Description of the Drawings, where the correlation between
                multiple sequences in the drawing and their sequence identifiers in the
                Brief Description is clear. A sequence found in a drawing sheet is not
                a ``Sequence Listing'' under Sec. 1.821(c) or (e). Therefore, a
                separate ``Sequence Listing'' would be required to comply with Sec.
                1.821(c). If the ``Sequence Listing'' was submitted as a PDF image file
                via the USPTO patent electronic filing system or on physical sheets of
                paper, a separate CRF of the ``Sequence Listing'' would be required to
                comply with Sec. 1.821(e).
                 Section 1.821(e)(1) is proposed to be added to set forth the
                requirements in Sec. 1.821(e)(1)(i) for submission of a CRF of the
                ``Sequence Listing,'' in compliance with Sec. 1.824, when a ``Sequence
                Listing'' was submitted as a PDF image file via the USPTO patent
                electronic filing system or on physical sheets of paper for an
                application filed under 35 U.S.C. 111(a). The proposed rule (Sec.
                1.821(e)(1)(ii)) also indicates that a statement is required to confirm
                that the CRF is identical to the ``Sequence Listing'' under Sec.
                1.821(c), when the submission of the ``Sequence Listing'' under Sec.
                1.821(c) was on physical sheets of paper or as a PDF image file via the
                USPTO patent electronic filing system.
                 Section 1.821(e)(2) is proposed to be added to set forth the
                requirements where the ``Sequence Listing'' under Sec. 1.821(c) in an
                application submitted under 35 U.S.C. 371 is in a PDF file (Sec.
                1.821(c)(2)) or on physical sheets of paper (Sec. 1.821(c)(3)), and
                not also as an ASCII plain text file, in compliance with Sec. 1.824
                (Sec. 1.821(c)(1)). In such situations, the following are required:
                (1) A copy of the ``Sequence Listing'' in CRF, in accordance with the
                requirements of Sec. 1.824 (Sec. 1.821(e)(2)(i)); and (2) a statement
                that the sequence information contained in the CRF, submitted under
                Sec. 1.821(e)(2)(i), is identical to the sequence information
                contained in the ``Sequence Listing'' submitted as a PDF image file
                (1.821(c)(2)) or on physical sheets of paper (1.821(c)(3)).
                 Section 1.821(e)(3) is proposed to be added to set forth the
                requirements where a ``Sequence Listing'' in ASCII plain text format,
                in compliance with Sec. 1.824, has not been submitted for an
                international application under the Patent Cooperation Treaty (PCT);
                this application contains disclosures of nucleotide and/or amino acid
                sequences, as defined in paragraph (a) of this section and is to be
                searched by the United States International Searching Authority or
                examined by the United States International Preliminary Examining
                Authority. In such situations, the following are required: (1) A copy
                of the ``Sequence Listing'' in CRF, in accordance with the requirements
                of Sec. 1.824 (Sec. 1.821(e)(3)(i)); (2) a late furnishing fee for
                providing a ``Sequence Listing'' in response to an invitation, as set
                forth in Sec. 1.445(a)(5) (Sec. 1.821(e)(3)(ii)); and (3) a statement
                that the sequence information contained in the CRF submitted under
                Sec. 1.821(e)(3)(i) does not go beyond the disclosure in the
                international application as filed, or a statement that the information
                recorded in the ASCII plain text file submitted under Sec.
                1.821(e)(3)(i) is identical to the sequence listing contained in the
                international application as filed, as applicable (Sec.
                1.821(e)(3)(iii)).
                 Section 1.821(e)(4) is proposed to be added to state that the CRF
                may not be retained as a part of the patent application file.
                 Section 1.821(f) is proposed to be reserved. The text previously
                found in this section is now in Sec. 1.821(e)(2)(iii).
                 Section 1.821(g) is proposed to be revised to delete reference to
                Sec. 1.821(f). Additionally, Sec. 1.821(g) is proposed to be revised
                to state that any amendment to add or replace a ``Sequence Listing''
                and CRF copy thereof must be submitted in accordance with the
                requirements of Sec. 1.825.
                 Section 1.821(h) is proposed to be revised to reference paragraphs
                (e)(3) of this section instead of paragraphs (b) through (f). Section
                1.821(h) is also proposed to be revised to add that a late furnishing
                fee, as set forth in Sec. 1.445(a)(5), is required where a ``Sequence
                Listing'' under PCT Rule 13ter is provided.
                 Section 1.822: Section 1.822(b) is proposed to be revised to remove
                all prior references to WIPO Standard ST.25 (1998) and instead cross-
                reference new Appendices A through F to part 1 of 37 CFR, subpart G,
                which would contain the updated 2009 version of the standard.
                Therefore, the statement regarding permission for incorporation by
                reference and information about the availability of ST.25 from WIPO's
                website is deleted.
                 Section 1.822(c)(1) is proposed to be revised to remove the prior
                reference to WIPO Standard ST.25 (1998) and instead cross-reference new
                Appendix A to part 1 of 37 CFR, subpart G, which would contain the
                updated 2009 version of the standard.
                 Section 1.822(c)(3) is proposed to be rewritten to replace
                instances of ``typed'' with ``listed.''
                 Section 1.822(c)(5) is proposed to be rewritten to replace
                ``presented'' with ``represented.''
                 Section 1.822(c)(6) is proposed to be rewritten to delete ``be
                marked'' and instead state ``appear.''
                [[Page 28308]]
                 Section 1.822(d)(1) is proposed to be revised to remove the prior
                reference to WIPO Standard ST.25 (1998) and instead cross-reference new
                Appendix C to part 1 of 37 CFR, subpart G, which would contain the
                updated 2009 version of the standard. When providing reference to the
                sequence in the text of the description or claims, the numeric sequence
                identifier is preceded by SEQ ID NO: Or the like, even if the actual
                sequence is also embedded in the text of the description or claims of
                the patent application. The use of SEQ ID NO: Is preferred but
                including ``or the like'' is intended to ensure that a formalities
                notice is not sent when an application uses, for example, ``SEQ NO.''
                or ``Seq. Id. No.'' or any similar identification for an amino acid or
                nucleotide sequence in the specification or claims where it is clear
                that a sequence from the ``Sequence Listing'' is shown in the
                description or claims.
                 Section 1.822(d)(3) is proposed to be rewritten to replace
                ``presented'' with ``represented.''
                 Section 1.822(d)(4) is proposed to be rewritten to replace
                ``presented'' with ``represented.''
                 Section 1.822(d)(5) is proposed to be rewritten to replace the
                second occurrence of ``presented'' with ``represented.''
                 Section 1.822(e) is proposed to be rewritten to replace ``that is
                made up'' with the term ``composed.''
                 Section 1.823: The title of Sec. 1.823 is proposed to be rewritten
                as ``Requirements for content of a `Sequence Listing' part of the
                specification.''
                 Section 1.823(a) is proposed to be rewritten to enumerate in Sec.
                1.823(a)(1) through (8) the content requirements for a ``Sequence
                Listing'' previously contained in Sec. Sec. 1.821(c), 1.823(a)(1),
                1.823(a)(2), and 1.823(b). Such requirements include, but are not
                limited to, sequence identifiers, the order and presentation of items
                of information, mandatory and optional information, the format as to
                line spacing, and the use of numeric identifiers.
                 Section 1.823(b)(1) is proposed to include a requirement for
                applications other than an international application in the
                international stage to contain an express incorporation by reference of
                the material submitted as an ASCII plain text file via the USPTO patent
                electronic filing system or on read-only optical disc(s) into the
                specification of the patent application to identify the name of the
                file, the date of creation, and the size of the file in bytes.
                 Section 1.823(b)(2) is proposed to specifically exempt the
                incorporation by reference requirement in Sec. 1.823(b)(1) from
                international applications during the international stage.
                 Section 1.823(b)(3) is proposed to be added to specifically set
                forth the format and content for a ``Sequence Listing'' that is
                submitted either as a PDF image file via the USPTO patent electronic
                filing system or on physical sheets of paper, as enumerated in Sec.
                1.823(b)(3)(i) through (vi).
                 Section 1.824: The title of Sec. 1.824 is proposed to be rewritten
                as ``Form and format for a nucleotide and/or amino acid sequence
                submission as an ASCII plain text file.''
                 Section 1.824(a) is proposed to be reorganized for clarity and to
                apply to any ``Sequence Listing'' submission as an ASCII plain text
                file, rather than only to the CRF of a ``Sequence Listing.'' Section
                1.824(a)(1) is proposed to set forth the computer compatibilities and
                operating systems permitted. Section 1.824(a)(2) is proposed to
                indicate that ASCII plain text is required to be used, that all
                printable characters are permitted, and that no nonprintable characters
                are permitted, except ASCII Carriage Return plus ASCII Line Feed (CRLF)
                or Line Feed (LF) as line terminators. Section 1.824(a)(3) is proposed
                to set forth the naming convention for the ASCII plain text file of the
                ``Sequence Listing.'' Section 1.824(a)(4) is proposed to indicate that
                no more than 74 printable characters can be present on any given line.
                This number represents a change from current rules (where 72 characters
                are permitted). This change is intended to conform to the number of
                characters of a sequence listing as printed in a granted patent or a
                pre-grant publication.
                 Section 1.824(a)(5) is proposed to indicate that pagination is not
                permitted and that the ASCII plain text file must be one continuous
                file with no hard page breaks and no page numbering.
                 Section 1.824(b) is proposed to indicate that the ASCII plain text
                file must contain a copy of a single ``Sequence Listing'' in a single
                file and may be submitted through either the USPTO patent electronic
                filing system or on read-only optical disc(s), in compliance with Sec.
                1.52(e). Section 1.824(b)(2) is proposed to provide that file
                compression may be used and to define the parameters for file
                compression for submission on a read-only optical disc. Section 1.824
                is proposed to be further revised to eliminate obsolete media on which
                the CRF of a ``Sequence Listing'' may be submitted. Section 1.824(c) is
                proposed to be eliminated, since the types of media available are
                specifically enumerated in Sec. 1.52(e). Section 1.824(d) is proposed
                to be eliminated, since the same provision is now included in Sec.
                1.52(e)(6).
                 Section 1.825: Sections 1.825(a) and (b) are proposed to be
                rewritten to distinguish between a newly added ``Sequence Listing'' and
                an amended/replacement ``Sequence Listing'' submission, respectively.
                Sections 1.825(a) and (b) are proposed to be rewritten to state when a
                new or amended/replacement copy of the CRF is also required upon
                submission of a ``Sequence Listing.''
                 Section 1.825(a) is proposed to be amended to provide for
                submission of a ``Sequence Listing'' not present on the application
                filing date (1) as an ASCII plain text file via either the USPTO patent
                electronic filing system or on a read-only optical disc, (2) as a PDF
                image file via the USPTO patent electronic filing system, or (3) on
                physical sheets of paper. The amendment adding the ``Sequence Listing''
                must include a request that the amendment be made in one of two ways.
                First, a ``Sequence Listing'' submitted as an ASCII plain text file (in
                accordance with Sec. 1.825(a)(2)(i)) must be incorporated by reference
                in a separate paragraph of the specification. Second, a ``Sequence
                Listing'' submitted as a PDF image file via the USPTO patent electronic
                filing system (in accordance with Sec. 1.825(a)(2)(ii)) or on physical
                sheets of paper (in accordance with Sec. 1.825(a)(2)(iii)) must be
                placed after the abstract of the disclosure. Additionally, the
                ``Sequence Listing'' must be submitted together with two statements.
                The first statement must indicate the basis for the amendment, with
                specific references to particular parts of the application as
                originally filed (specification, claims, drawings) for all sequence
                data in the ``Sequence Listing'' (Sec. 1.821(a)(3)). The second
                statement must indicate that the ``Sequence Listing'' contains no new
                matter (Sec. 1.821(a)(4)). Finally, if needed, Sec. 1.825(a)(5)
                provides that a new or substitute CRF must be submitted together with a
                statement, pursuant to Sec. 1.825(a)(6), that the sequence information
                contained in the CRF is the same as the sequence information contained
                in the ``Sequence Listing'' that had been submitted as a PDF image file
                via the USPTO patent electronic filing system or on physical sheets of
                paper.
                 Section 1.825(b) is proposed to be updated to require an amended/
                replacement ``Sequence Listing'' submitted: (1) As an ASCII plain text
                file via either the USPTO patent electronic filing system or on a read-
                [[Page 28309]]
                only optical disc (Sec. 1.825(b)(1)(i)), (2) as a PDF image file via
                the USPTO patent electronic filing system (Sec. 1.825(b)(1)(ii)), or
                (3) on physical sheets of paper (Sec. 1.825(b)(1)(iii)). The amended/
                replacement ``Sequence Listing'' must include a request that it be made
                in one of two ways. First, a request that the amended/replacement
                ``Sequence Listing,'' submitted as an ASCII plain text file, is
                incorporated by reference in a separate paragraph of the specification
                (replacing any prior such paragraph, as applicable) (Sec.
                1.825(b)(2)). The second way for such a request is by placing, after
                the abstract of the disclosure, the amended/replacement ``Sequence
                Listing'' that was submitted as a PDF image file via the USPTO patent
                electronic filing system or on physical sheets of paper (replacing any
                prior ``Sequence Listing,'' as applicable).
                 The amended/replacement ``Sequence Listing'' must be submitted
                together with three statements. The first statement must identify the
                location of all deletions, replacements, or additions to the ``Sequence
                Listing'' (Sec. 1.825(b)(3)). The second statement must indicate the
                basis for the amendment, with specific references to particular parts
                of the application as originally filed (specification, claims,
                drawings) for all amended sequence data in the replacement ``Sequence
                Listing'' (Sec. 1.825(b)(4)). The third statement must indicate that
                the replacement ``Sequence Listing'' contains no new matter (Sec.
                1.825(b)(5)). Finally, if needed, a new or substitute CRF with the
                amendment incorporated therein (Sec. 1.825(b)(6)) must be submitted
                together with a statement that the sequence information contained in
                the CRF is the same as the sequence information contained in the
                replacement ``Sequence Listing'' submitted as a PDF image file via the
                USPTO patent electronic filing system or on physical sheets of paper
                (Sec. 1.825(b)(7)).
                 Section 1.825(c) is proposed to replace current Sec. 1.825(c),
                which is proposed to be moved to Sec. 1.825(d). Section 1.825(c)
                relates to the required incorporation by reference statement when
                submitting a ``Sequence Listing'' under Sec. 1.821(c)(1). Should the
                application as originally filed not contain the incorporation by
                reference, then the application must be amended to contain such an
                incorporation by reference.
                 Section 1.825(d) is proposed to contain the material from current
                Sec. 1.825(c).
                 Subpart G of part 1: Appendices A through F are proposed to be
                added, explicitly incorporating the text of Tables 1-6, Appendix 2,
                WIPO Standard ST.25 (2009) into the CFR. Appendix G is proposed to be
                added to incorporate the table that was previously located in Sec.
                1.823.
                Rulemaking Considerations
                 A. Administrative Procedure Act: The changes proposed in this
                rulemaking involve rules of agency practice and procedure, and/or
                interpretive rules. See Bachow Commc'ns Inc. v. FCC, 237 F.3d 683, 690
                (D.C. Cir. 2001) (rules governing an application process are procedural
                under the Administrative Procedure Act); Inova Alexandria Hosp. v.
                Shalala, 244 F.3d 342, 350 (4th Cir. 2001) (rules for handling appeals
                are procedural where they do not change the substantive standard for
                reviewing claims); Nat'l Org. of Veterans' Advocates v. Sec'y of
                Veterans Affairs, 260 F.3d 1365, 1375 (Fed. Cir. 2001) (rule that
                clarifies interpretation of a statute is interpretive).
                 Accordingly, prior notice and opportunity for public comment for
                the changes proposed in this rulemaking are not required pursuant to 5
                U.S.C. 553(b) or (c), or any other law. See Cooper Techs. Co. v. Dudas,
                536 F.3d 1330, 1336-37 (Fed. Cir. 2008) (stating that 5 U.S.C. 553, and
                thus 35 U.S.C. 2(b)(2)(B), do not require notice and comment rulemaking
                for ``interpretative rules, general statements of policy, or rules of
                agency organization, procedure, or practice'' (quoting 5 U.S.C.
                553(b)(A))). However, the USPTO has chosen to seek public comment
                before implementing the rule to benefit from the public's input.
                 B. Regulatory Flexibility Act: Under the Regulatory Flexibility Act
                (5 U.S.C. 601 et seq.), whenever an agency is required by 5 U.S.C. 553
                (or any other law) to publish a notice of proposed rulemaking (NPRM),
                the agency must prepare and make available for public comment an
                Initial Regulatory Flexibility Analysis, unless the agency certifies
                under 5 U.S.C. 605(b) that the proposed rule, if implemented, will not
                have a significant economic impact on a substantial number of small
                entities. 5 U.S.C. 603, 605.
                 For the reasons set forth herein, the Senior Counsel for Regulatory
                and Legislative Affairs of the USPTO has certified to the Chief Counsel
                for Advocacy of the Small Business Administration that this rule will
                not have a significant economic impact on a substantial number of small
                entities. See 5 U.S.C. 605(b).
                 The USPTO proposes to amend the rules of practice to permit higher-
                capacity physical media to be submitted to accommodate patent
                applications for certain inventions that require significant data in
                ASCII text format that exceed the capacity of the Office's electronic
                filing system. Additionally, extraction of compressed data files, which
                had not been permitted in the past for certain submissions, would be
                permitted if compliant with certain proposed new procedures. Other
                rules relating to certain obsolete and non-secure methods of presenting
                data would be eliminated. Lastly, this NPRM would remove an applicant's
                ability to rely on a previously submitted CRF of required sequence
                information (i.e., CRF transfer requests are eliminated). In light of
                the availability to download a ``Sequence Listing'' from granted U.S.
                patents and U.S. patent application publications via Public PAIR in the
                Supplemental Content tab, there is no longer a need for a CRF transfer.
                 This rulemaking would make more flexible the process for submitting
                large amounts of data and streamline other procedural steps related to
                data files associated with patent applications. This rulemaking's
                proposed changes are largely procedural in nature, and do not impose
                any additional requirements or fees on applicants. For the foregoing
                reasons, the changes proposed in this NPRM will not have a significant
                economic impact on a substantial number of small entities.
                 C. Executive Order 12866 (Regulatory Planning and Review): This
                rulemaking has been determined to be not significant for purposes of
                Executive Order 12866 (Sept. 30, 1993).
                 D. Executive Order 13563 (Improving Regulation and Regulatory
                Review): The USPTO has complied with Executive Order 13563 (Jan. 18,
                2011). Specifically, to the extent feasible and applicable, the USPTO
                has: (1) Reasonably determined that the benefits of the rule justify
                its costs; (2) tailored the rule to impose the least burden on society
                consistent with obtaining the agency's regulatory objectives; (3)
                selected a regulatory approach that maximizes net benefits; (4)
                specified performance objectives; (5) identified and assessed available
                alternatives; (6) involved the public in an open exchange of
                information and perspectives among experts in relevant disciplines,
                affected stakeholders in the private sector, and the public as a whole,
                and provided online access to the rulemaking docket; (7) attempted to
                promote coordination, simplification, and harmonization across
                government agencies and identified goals designed to promote
                innovation; (8) considered approaches that reduce burdens while
                maintaining flexibility and freedom of choice for the public; and (9)
                ensured
                [[Page 28310]]
                the objectivity of scientific and technological information and
                processes.
                 E. Executive Order 13132 (Federalism): This rulemaking does not
                contain policies with federalism implications sufficient to warrant
                preparation of a Federalism Assessment under Executive Order 13132
                (Aug. 44, 1999).
                F. Executive Order 13175 (Tribal Consultation): This rulemaking
                will not (1) have substantial direct effects on one or more Indian
                tribes; (2) impose substantial direct compliance costs on Indian tribal
                governments; or (3) preempt tribal law. Therefore, a tribal summary
                impact statement is not required under Executive Order 13175 (Nov. 6,
                2000).
                 G. Executive Order 13211 (Energy Effects): This rulemaking is not a
                significant energy action under Executive Order 13211 because this
                rulemaking is not likely to have a significant adverse effect on the
                supply, distribution, or use of energy. Therefore, a Statement of
                Energy Effects is not required under Executive Order 13211 (May 18,
                2001).
                 H. Executive Order 12988 (Civil Justice Reform): This rulemaking
                meets applicable standards to minimize litigation, eliminate ambiguity,
                and reduce burden as set forth in sections 3(a) and 3(b)(2) of
                Executive Order 12988 (Feb. 55, 1996).
                I. Executive Order 13045 (Protection of Children): This rulemaking
                does not concern an environmental risk to health or safety that may
                disproportionately affect children under Executive Order 13045 (Apr.
                21, 1997).
                 J. Executive Order 12630 (Taking of Private Property): This
                rulemaking will not effect a taking of private property or otherwise
                have taking implications under Executive Order 12630 (Mar. 15, 1988).
                 K. Congressional Review Act: Under the Congressional Review Act
                provisions of the Small Business Regulatory Enforcement Fairness Act of
                1996 (5 U.S.C. 801 et seq.), prior to issuing any final rule, the USPTO
                will submit a report containing the final rule and other required
                information to the United States Senate, the United States House of
                Representatives, and the Comptroller General of the Government
                Accountability Office. The changes in this rulemaking are not expected
                to result in an annual effect on the economy of $100 million or more, a
                major increase in costs or prices, or significant adverse effects on
                competition, employment, investment, productivity, innovation, or the
                ability of United States-based enterprises to compete with foreign-
                based enterprises in domestic and export markets. Therefore, this
                rulemaking is not expected to result in a ``major rule'' as defined in
                5 U.S.C. 804(2).
                 L. Unfunded Mandates Reform Act of 1995: The changes set forth in
                this rulemaking do not involve a Federal intergovernmental mandate that
                will result in the expenditure by State, local, and tribal governments,
                in the aggregate, of $100 million (as adjusted) or more in any one
                year, or a Federal private sector mandate that will result in the
                expenditure by the private sector of $100 million (as adjusted) or more
                in any one year, and will not significantly or uniquely affect small
                governments. Therefore, no actions are necessary under the provisions
                of the Unfunded Mandates Reform Act of 1995. See 2 U.S.C. 1501 et seq.
                 M. National Environmental Policy Act of 1969: This rulemaking will
                not have any effect on the quality of the environment and is thus
                categorically excluded from review under the National Environmental
                Policy Act of 1969. See 42 U.S.C. 4321 et seq.
                 N. National Technology Transfer and Advancement Act of 1995: The
                requirements of section 12(d) of the National Technology Transfer and
                Advancement Act of 1995 (15 U.S.C. 272 note) are not applicable because
                this rulemaking does not contain provisions that involve the use of
                technical standards.
                 O. Paperwork Reduction Act of 1995: The Paperwork Reduction Act of
                1995 (44 U.S.C. 3501-3549) requires that the USPTO consider the impact
                of paperwork and other information collection burdens imposed on the
                public. In accordance with section 3507(d) of the Paperwork Reduction
                Act of 1995, the majority of the paperwork and other information
                collection burdens discussed in this proposed rule have already been
                approved under the following Office of Management and Budget (OMB)
                Control Numbers: 0651-0024 (Sequence Listing), 0651-0031 (Patent
                Processing), 0651-0032 (Initial Patent Applications), and 0651-0064
                (Patent Reexaminations and Supplemental Examinations).
                 Modifications to 0651-0024 because of this proposed rulemaking will
                be submitted to OMB for approval prior to this rule becoming effective.
                Modifications include the removal of the Request for Transfer of a
                Computer Readable Form Under 37 CFR 1.821(e) (PTO/SB/93), which will
                result in a slight reduction in burden associated with this information
                collection. The USPTO estimates that this information collection's
                annual burden will decrease by 1,550 responses and 155 burden hours.
                These burden estimates are based on the current OMB approved burdens
                (response volumes) associated with this information collection, which
                may be different from any forecasts mentioned in other parts of this
                proposed rule.
                 The changes discussed in this proposed rule do not affect the
                information collection requirements or burdens associated with 0651-
                0031, 0651-0032 and 0651-0064 listed above; therefore, the USPTO does
                not plan to take any additional actions on these information
                collections as a result of this rulemaking. Notwithstanding any other
                provision of law, no person is required to respond to, nor shall a
                person be subject to a penalty for failure to comply with, a collection
                of information subject to the requirements of the Paperwork Reduction
                Act unless that collection of information has a currently valid OMB
                control number.
                 P. E-Government Act Compliance: The USPTO is committed to
                compliance with the E-Government Act to promote the use of the internet
                and other information technologies, to provide increased opportunities
                for citizen access to Government information and services, and for
                other purposes.
                List of Subjects in 37 CFR Part 1
                 Administrative practice and procedure, Biologics, Courts, Freedom
                of information, Inventions and patents, Reporting and recordkeeping
                requirements, Small businesses.
                 For the reasons stated in the preamble and under the authority
                contained in 35 U.S.C. 2, as amended, the USPTO proposes to amend 37
                CFR part 1 as follows:
                PART 1--RULES OF PRACTICE IN PATENT CASES
                0
                1. The authority citation for 37 CFR part 1 continues to read as
                follows:
                 Authority: 35 U.S.C. 2(b)(2), unless otherwise noted.
                0
                2. Amend Sec. 1.52 by revising the heading and paragraphs (e) and (f)
                to read as follows:
                Sec. 1.52 Language, paper, writing, margins, read-only optical disc
                specifications.
                * * * * *
                 (e) Electronic documents submitted on a read-only optical disc that
                are to become part of the permanent United States Patent and Trademark
                Office records in the file of a patent application, reexamination, or
                supplemental examination proceeding. (1) The following documents may be
                submitted to the Office on a read-only
                [[Page 28311]]
                optical disc in compliance with this paragraph:
                 (i) A ``Computer Program Listing Appendix'' (see Sec. 1.96(c));
                 (ii) A ``Sequence Listing'' (submitted under Sec. 1.821(c) in
                compliance with Sec. 1.824); or
                 (iii) ``Large Tables'' (see Sec. 1.58(c)).
                 (2) Read-only optical disc as used in this part means a finalized
                disc in conformance with International Organization for Standardization
                (ISO) 9660, on which the data is recorded so it is permanent and cannot
                be changed or erased, and is one of:
                 (i) Compact Disc-Read-Only Memory (CD-ROM) or a Compact Disc-
                Recordable (CD-R); or
                 (ii) Digital Video Disc-Recordable (DVD-R or DVD+R);
                 (3) Each read-only optical disc must conform to the following
                requirements:
                 (i) Computer compatibility: PC or Mac[supreg];
                 (ii) Operating system compatibility: MS-DOS[supreg], MS-
                Windows[supreg], MacOS[supreg], or Unix[supreg]/Linux[supreg];
                 (iii) The contents of each read-only optical disc must be in
                American Standard Code for Information Interchange (ASCII) plain text
                and if compressed, must be compressed in accordance with Sec. Sec.
                1.58, 1.96, and 1.824, as applicable.
                 (4) Each read-only optical disc must be enclosed in a hard case
                within an unsealed, padded, and protective mailing envelope, and must
                be accompanied by a transmittal letter in accordance with paragraph (a)
                of this section, including the following information:
                 (i) First-named inventor (if known);
                 (ii) Title of the invention;
                 (iii) Attorney docket or file reference number (if applicable);
                 (iv) Application number and filing date (if known);
                 (v) The operating system (MS-DOS[supreg], MS-Windows[supreg], Mac
                OS[supreg], or Unix[supreg]/Linux[supreg]) used to produce the disc;
                and
                 (vi) The file(s) contained on the read-only optical disc, including
                the name of the file, the size of the file in bytes, and the date of
                creation.
                 (5) Each read-only optical disc must have a label permanently
                affixed thereto on which the following information has been hand-
                printed or typed:
                 (i) First-named inventor (if known);
                 (ii) Title of the invention;
                 (iii) Attorney docket or file reference number (if applicable);
                 (iv) Application number and filing date (if known);
                 (v) Date on which the data were recorded on the read-only optical
                disc; and
                 (vi) Disc order (e.g., ``1 of X''), if multiple read-only optical
                discs are submitted.
                 (6) Read-only optical discs will not be returned to the applicant
                and may not be retained as part of the patent application file.
                 (7) Any amendment to the information on a read-only optical disc
                must be by way of a replacement read-only optical disc, in compliance
                with Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a
                ``Computer Program Listing Appendix,'' and Sec. 1.825(b) for a
                ``Sequence Listing'' or Computer Readable Form (CRF) of a ``Sequence
                Listing.''
                 (8) The specification must contain an incorporation by reference of
                the material on each read-only optical disc in a separate paragraph
                (Sec. 1.77(b)(5)), identifying the name of each file, their date of
                creation, and their size in bytes, except for an international
                application in the international stage. The Office may require the
                applicant to amend the specification to include the material
                incorporated by reference.
                 (9) If a file is unreadable, it will be treated as not having been
                submitted, and a notice will be issued to supply a compliant
                submission.
                 (f) Determining application size fees for applications containing
                electronic documents submitted on a read-only optical disc or via the
                USPTO patent electronic filing system--(1) Submission on Read-Only
                Optical Discs: The application size fee required by Sec. 1.16(s) or
                1.492(j), for an application component submitted in part on a read-only
                optical disc in compliance with paragraph (e) of this section, shall be
                determined such that each three kilobytes of content submitted on a
                read-only optical disc shall be counted as a sheet of paper. Excluded
                from this determination is any ASCII plain text file submitted on a
                read-only optical disc under paragraph (e) of this section containing:
                 (i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing'' in
                compliance with Sec. 1.821(c) or (e); or
                 (ii) Any ``Computer Program Listing Appendix'' in compliance with
                Sec. 1.96(c).
                 (2) Submission via the USPTO Patent Electronic Filing System: The
                application size fee required by Sec. 1.16(s) or 1.492(j), for an
                application submitted in whole or in part via the USPTO patent
                electronic filing system, shall be determined such that the paper size
                equivalent will be considered to be 75% of the number of sheets of
                paper present in the specification and drawings of the application when
                entered into the Office file wrapper after being rendered by the USPTO
                patent electronic filing system. Excluded from this determination is
                any ASCII plain text file submitted via the USPTO patent electronic
                filing system containing:
                 (i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing,'' in
                compliance with Sec. 1.821(c) or (e); or
                 (ii) Any ``Computer Program Listing Appendix'' in compliance with
                Sec. 1.96(c).
                 (3) Any submission of a ``Sequence Listing'' in electronic form of
                300 MB-800 MB filed in an application under 35 U.S.C. 111 or 371 will
                be subject to the fee set forth in Sec. 1.21(o)(1). Any submission of
                a ``Sequence Listing'' filed in electronic form that exceeds 800 MB in
                an application under 35 U.S.C. 111 or 371 will be subject to the fee
                set forth in Sec. 1.21(o)(2).
                0
                3. Amend Sec. 1.58 by revising paragraphs (b) and (c) and adding
                paragraphs (d) through (j) to read as follows:
                Sec. 1.58 Chemical and mathematical formulas and tables.
                * * * * *
                 (b) Chemical and mathematical formulas and tables must be presented
                in compliance with Sec. 1.52(a) and (b), except that chemical and
                mathematical formulas or tables may be placed in a landscape
                orientation if they cannot be presented satisfactorily in a portrait
                orientation. Typewritten characters used in such formulas and tables
                must be chosen from a block (nonscript) type font or lettering style
                having capital letters that should be at least 0.422 cm (0.166 inches)
                high (e.g., preferably Arial, Times Roman, or Courier, with a font size
                of 12 point), but may be no smaller than 0.21cm (0.08 inches) high
                (e.g., a font size of 6 point). A space at least 0.64 cm (0.25 inches)
                high should be provided between complex formulas and tables and the
                text. Chemical and mathematical formulas must be configured to maintain
                the proper positioning of their characters when displayed in order to
                preserve their intended meaning. Tables should have the lines and
                columns of data closely spaced to conserve space, consistent with a
                high degree of legibility.
                 (c) The following ``Large Tables'' may be submitted in electronic
                form in ASCII plain text via the USPTO patent electronic filing system
                or on a read-only optical disc, in compliance with Sec. 1.52(e),
                excluding an international application during the international stage:
                 (1) Any individual table that is more than 50 pages in length; or
                 (2) Multiple tables, if the total number of pages of all the tables
                in an
                [[Page 28312]]
                application exceeds 100 pages in length, where a table page is a page
                printed on paper, in conformance with paragraph (b) of this section.
                 (d) ``Large Tables'' submitted in electronic form in ASCII plain
                text must conform to the following requirements:
                 (1) Must maintain the spatial relationships (e.g., alignment of
                columns and rows) of the table elements when displayed to visually
                preserve the relational information they convey.
                 (2) Must have the following compatibilities:
                 (i) Computer compatibility: PC or Mac[supreg];
                 (ii) Operating system compatibility: MS-DOS[supreg], MS-
                Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
                 (3) Must be in ASCII plain text, where:
                 (i) All printable characters (including the space character) are
                permitted;
                 (ii) No nonprintable (ASCII control) characters are permitted,
                except ASCII Carriage Return plus ASCII Line Feed (CRLF) or Line Feed
                (LF) as line terminators.
                 (4) Must be named as *.txt, where ``*'' is one character or a
                combination of characters limited to upper- or lowercase letters,
                numbers, hyphens, and underscores and does not exceed 60 characters in
                total, excluding the extension. No spaces or other types of characters
                are permitted in the file name.
                 (5) Must be incorporated by reference in a separate paragraph of
                the specification, in accordance with Sec. 1.77(b)(5).
                 (e) ``Large Tables'' submitted via the USPTO patent electronic
                filing system must not exceed 25 MB, and file compression is not
                permitted.
                 (f) ``Large Tables'' submitted in compliance with Sec. 1.52(e) via
                read-only optical disc, must meet the following requirements:
                 (1) The ASCII plain text file may be compressed using
                WinZip[supreg], 7-Zip, or Unix[supreg]/Linux[supreg] Zip;
                 (2) A compressed file must not be self-extracting; and
                 (3) A compressed ASCII plain text file that does not fit on a
                single read-only optical disc may be split into multiple file parts in
                accordance with the target read-only optical disc size and labeled in
                compliance with Sec. 1.52(e)(5)(vi).
                 (g) Any amendments to ``Large Tables'' in electronic form in ASCII
                plain text format must include:
                 (1) A replacement ASCII plain text file, in accordance with the
                requirements of paragraphs (d) through (f) of this section, submitted
                via the USPTO patent electronic filing system or on a read-only optical
                disc, in compliance with Sec. 1.52(e), labeled as ``REPLACEMENT MM/DD/
                YYYY'' (with the month, day, and year of creation indicated);
                 (2) A request that the amendment be made by incorporation by
                reference of the material in the replacement ASCII plain text file, in
                a separate paragraph of the specification (replacing any prior such
                paragraph, as applicable) identifying the name of the file, the date of
                creation, and the size of the file in bytes (see Sec. 1.77(b)(5));
                 (3) A statement that identifies the location of all deletions,
                replacements, or additions to the ASCII plain text file; and
                 (4) A statement that the replacement ASCII plain text file contains
                no new matter.
                 (h) The specification of an application with ``Large Tables'' as an
                ASCII plain text file, present on the application filing date, without
                an incorporation by reference of the material contained in the ASCII
                plain text file, must be amended to contain a separate paragraph
                incorporating by reference the material contained in the ASCII plain
                text file, in accordance with Sec. 1.77(b)(5).
                 (i) Any read-only optical disc for ``Large Tables'' must be
                submitted in duplicate. The read-only optical disc and duplicate copy
                must be labeled ``Copy 1'' and ``Copy 2,'' respectively. The
                transmittal letter that accompanies the read-only optical discs must
                include a statement that the two read-only optical discs are identical.
                In the event that the two read-only optical discs are not identical,
                the Office will use the read-only optical disc labeled ``Copy 1'' for
                further processing.
                 (j) Any amendment to the information on a read-only optical disc
                must be by way of a replacement read-only optical disc, in compliance
                with Sec. 1.58(g), where the replacement read-only optical disc and
                copy must be labeled ``COPY 1 REPLACEMENT MM/DD/YYYY'' (with the month,
                day, and year of creation indicated), and ``COPY 2 REPLACEMENT MM/DD/
                YYYY,'' respectively.
                0
                4. Amend Sec. 1.71 by revising paragraph (f) to read as follows:
                Sec. 1.71 Detailed description and specification of the invention.
                * * * * *
                 (f) The specification must commence on a separate sheet. Each sheet
                including part of the specification may not include other parts of the
                application or other information. The claim(s), abstract, and
                ``Sequence Listing'' (if required or submitted under Sec. 1.821(c))
                should not be included on a sheet including any other part of the
                application.
                * * * * *
                0
                5. Amend Sec. 1.77 by revising paragraphs (b)(5) and (13) to read as
                follows:
                Sec. 1.77 Arrangement of application elements.
                * * * * *
                 (b) * * *
                 (5) An incorporation by reference statement regarding the material
                on the one or more ASCII plain text files, submitted via the USPTO
                patent electronic filing system or on one or more read-only optical
                discs (see Sec. 1.52(e)(8)), identifying the names of each file, the
                date of creation of each file, and the size of each file in bytes, for
                the following document types:
                 (i) A ``Computer Program Listing Appendix'' (see Sec. 1.96(c));
                 (ii) A ``Sequence Listing'' (see Sec. 1.821(c)); or
                 (iii) ``Large Tables'' (see Sec. 1.58(c)).
                * * * * *
                 (13) ``Sequence Listing,'' required by Sec. 1.821(c), that is
                submitted as a Portable Document Format (PDF) file (as set forth in
                Sec. 1.821(c)(1)(ii)) via the USPTO patent electronic filing system or
                on physical sheets of paper (as set forth in Sec. 1.821(c)(1)(iii)).
                * * * * *
                0
                6. Amend Sec. 1.96 by revising paragraphs (a) and (c) to read as
                follows:
                Sec. 1.96 Submission of computer program listings.
                 (a) General. Descriptions of the operation and general content of
                computer program listings should appear in the description portion of
                the specification. A computer program listing for the purpose of this
                section is defined as a document that lists in appropriate sequence the
                instructions, routines, and other contents of a program for a computer.
                The program listing may be either in machine or machine-independent
                (object or source) language that will cause a computer to perform a
                desired procedure or task such as solve a problem, regulate the flow of
                work in a computer, or control or monitor events. Computer program
                listings may be submitted in patent applications, as set forth in
                paragraphs (b) and (c) of this section.
                * * * * *
                 (c) As an appendix that will not be printed: Any computer program
                listing may, and any computer program listing having over 300 lines (up
                to 72 characters per line) must, be submitted as an electronic document
                in ASCII plain text, whether submitted via the
                [[Page 28313]]
                USPTO patent electronic filing system or on a read-only optical disc,
                in compliance with Sec. 1.52(e). An electronic document containing
                such a computer program listing is to be referred to as a ``Computer
                Program Listing Appendix.'' The ``Computer Program Listing Appendix''
                will not be part of the printed patent. The specification must include
                an incorporation by reference of the ``Computer Program Listing
                Appendix,'' in accordance with Sec. 1.77(b)(5).
                 (1) A ``Computer Program Listing Appendix'' must conform to the
                following requirements:
                 (i) Computer compatibility: PC or Mac[supreg];
                 (ii) Operating system compatibility: MS-DOS[supreg], MS-
                Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg];
                 (iii) Line terminator: ASCII CRLF or LF only; and
                 (iv) Control Codes: The data must not be dependent on control
                characters or codes that are not defined in the ASCII character set.
                 (2) Each file must be named as *.txt, where ``*'' is one character
                or a combination of characters limited to upper- or lowercase letters,
                numbers, hyphens, and underscores and does not exceed 60 characters in
                total, excluding the extension. No spaces or other types of characters
                are permitted in the file name.
                 (3) Each file containing a ``Computer Program Listing Appendix''
                submitted via the USPTO patent electronic filing system must not exceed
                25 MB, and file compression is not permitted.
                 (4) A ``Computer Program Listing Appendix'' submitted in compliance
                with Sec. 1.52(e) must conform to the following requirements:
                 (i) A separate read-only optical disc containing a ``Computer
                Program Listing Appendix'' must be submitted for each applicable
                application;
                 (ii) Multiple computer program listings for a single application
                may be placed on a single read-only optical disc;
                 (iii) Multiple read-only optical discs, containing one or more
                computer program listings, may be submitted for a single application,
                if necessary;
                 (iv) Any computer program listing may, and a computer program
                listing having a nested file structure must, when submitted in
                compliance with Sec. 1.52(e), be compressed into a single file using
                WinZip[supreg], 7-Zip, or Unix[supreg]/Linux[supreg] Zip;
                 (v) Any compressed file must not be self-extracting; and
                 (vi) A compressed ASCII plain text file that does not fit on a
                single read-only optical disc may be split into multiple file parts, in
                accordance with the target read-only optical disc size and labeled in
                compliance with Sec. 1.52(e)(5)(vi).
                 (5) Any amendments to a ``Computer Program Listing Appendix'' in
                electronic form in ASCII plain text format must include:
                 (i) A replacement ASCII plain text file, in accordance with the
                requirements of paragraph (c) of this section, via the USPTO patent
                electronic filing system, or on a read-only optical disc, in compliance
                with Sec. 1.52(e) and labeled as ``COPY 1 REPLACEMENT MM/DD/YYYY''
                (with the month, day, and year of creation indicated) and ``COPY 2
                REPLACEMENT MM/DD/YYYY;''
                 (ii) A request that the amendment be made by incorporation by
                reference of the material in the replacement ASCII plain text file, in
                a separate paragraph of the specification (replacing any prior such
                paragraph) identifying the name of the file, the date of creation, and
                the size of the file in bytes (see Sec. 1.77(b)(5));
                 (iii) A statement that identifies the location of all deletions,
                replacements, or additions to the ASCII plain text file; and
                 (iv) A statement that the replacement ASCII plain text file
                contains no new matter.
                 (6) The specification of a complete application with a ``Computer
                Program Listing Appendix'' as an ASCII plain text file, filed on the
                application filing date, without an incorporation by reference of the
                material contained in the ASCII plain text file, must be amended to
                contain a separate paragraph incorporating by reference the material
                contained in the ASCII plain text file, in accordance with Sec.
                1.77(b)(5).
                 (7) Any read-only optical disc for a ``Computer Program Listing
                Appendix'' must be submitted in duplicate. The read-only optical disc
                and duplicate copy must be labeled ``Copy 1'' and ``Copy 2,''
                respectively. The transmittal letter that accompanies the read-only
                optical discs must include a statement that the two read-only optical
                discs are identical. In the event that the two read-only optical discs
                are not identical, the Office will use the read-only optical disc
                labeled ``Copy 1'' for further processing. Any amendment to the
                information on a read-only optical disc must be by way of a replacement
                read-only optical disc, in compliance with Sec. 1.96(c)(5).
                0
                7. Amend Sec. 1.121 by revising paragraph (b) introductory text and
                adding paragraph (b)(6) to read as follows:
                Sec. 1.121 Manner of making amendments in applications.
                * * * * *
                 (b) Specification. Amendments to the specification, other than the
                claims, ``Large Tables (Sec. 1.58(c)), a ``Computer Program Listing
                Appendix'' (Sec. 1.96(c)(5) and (7)), and a ``Sequence Listing'' or
                CRF (Sec. 1.825), must be made by adding, deleting, or replacing a
                paragraph; by replacing a section; or by a substitute specification, in
                the manner specified in this section.
                * * * * *
                 (6) Changes to ``Large Tables,'' a ``Computer Program Listing
                Appendix,'' or a ``Sequence Listing'' must be made in accordance with
                Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer
                Program Listing Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
                * * * * *
                0
                8. Amend Sec. 1.173 by revising paragraphs (b)(1) and (d) to read as
                follows:
                Sec. 1.173 Reissue specification, drawings, and amendments.
                * * * * *
                 (b) * * *
                 (1) Specification other than the claims, ``Large Tables'' (Sec.
                1.58(c)), a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), or a
                ``Sequence Listing'' (Sec. 1.821(c)). (i) Changes to the
                specification, other than to the claims, ``Large Tables'' (Sec.
                1.58(c)), a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), or a
                ``Sequence Listing'' (Sec. 1.821(c)), must be made by submission of
                the entire text of an added or rewritten paragraph, including markings
                pursuant to paragraph (d) of this section, except that an entire
                paragraph may be deleted by a statement deleting the paragraph, without
                presentation of the text of the paragraph. The precise point in the
                specification where any added or rewritten paragraph is located must be
                identified.
                 (ii) Changes to ``Large Tables,'' a ``Computer Program Listing
                Appendix,'' or a ``Sequence Listing'' must be made in accordance with
                Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer
                Program Listing Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
                * * * * *
                 (d) Changes shown by markings. Any changes relative to the patent
                being reissued that are made to the specification, including the claims
                but excluding ``Large Tables,'' a ``Computer Program Listing
                Appendix,'' or a ``Sequence Listing,'' upon filing or by an amendment
                paper in the reissue application, must include the following markings:
                [[Page 28314]]
                 (1) The matter to be omitted by reissue must be enclosed in
                brackets; and
                 (2) The matter to be added by reissue must be underlined.
                * * * * *
                0
                9. Amend Sec. 1.530 by revising paragraph (d)(1) to read as follows:
                Sec. 1.530 Statement by patent owner in ex parte reexamination;
                amendment by patent owner in ex parte or inter partes reexamination;
                inventorship change in ex parte or inter partes reexamination.
                * * * * *
                 (d) * * *
                 (1) Specification other than the claims, ``Large Tables'' (Sec.
                1.58(c)), a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), or a
                ``Sequence Listing'' (Sec. 1.821(c)).
                 (i) Changes to the specification, other than to the claims, ``Large
                Tables'' (Sec. 1.58(c)), a ``Computer Program Listing Appendix''
                (Sec. 1.96(c)), or a ``Sequence Listing'' (Sec. 1.821(c)), must be
                made by submission of the entire text of an added or rewritten
                paragraph, including markings pursuant to paragraph (f) of this
                section, except that an entire paragraph may be deleted by a statement
                deleting the paragraph, without presentation of the text of the
                paragraph. The precise point in the specification where any added or
                rewritten paragraph is located must be identified.
                 (ii) Changes to ``Large Tables,'' a ``Computer Program Listing
                Appendix,'' or a ``Sequence Listing'' must be made, in accordance with
                Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer
                Program Listing Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
                * * * * *
                0
                10. Amend Sec. 1.821 by revising paragraphs (a), and (c) through (e),
                removing and reserving paragraph (f), and revising paragraphs (g)
                through (h) to read as follows:
                Sec. 1.821 Nucleotide and/or amino acid sequence disclosures in
                patent applications.
                 (a) Nucleotide and/or amino acid sequences, as used in Sec. Sec.
                1.821 through 1.825, are interpreted to mean an unbranched sequence of
                4 or more amino acids or an unbranched sequence of 10 or more
                nucleotides. Branched sequences are specifically excluded from this
                definition. Sequences with fewer than four specifically defined
                nucleotides or amino acids are specifically excluded from this section.
                ``Specifically defined'' means those amino acids other than ``Xaa'' and
                those nucleotide bases other than ``n,'' defined in accordance with
                Appendices A through F to this subpart. Nucleotides and amino acids are
                further defined as follows:
                 (1) Nucleotides: Nucleotides are intended to embrace only those
                nucleotides that can be represented using the symbols set forth in
                Appendix A to this subpart. Modifications (e.g., methylated bases) may
                be described as set forth in Appendix B to this subpart, but shall not
                be shown explicitly in the nucleotide sequence.
                 (2) Amino acids: Amino acids are those L-amino acids commonly found
                in naturally occurring proteins and are listed in Appendix C to this
                subpart. Those amino acid sequences containing D-amino acids are not
                intended to be embraced by this definition. Any amino acid sequence
                that contains post-translationally modified amino acids may be
                described as the amino acid sequence that is initially translated using
                the symbols shown in Appendix C to this subpart with the modified
                positions (e.g., hydroxylations or glycosylations) being described as
                set forth in Appendix D to this subpart, but these modifications shall
                not be shown explicitly in the amino acid sequence. Any peptide or
                protein that can be expressed as a sequence using the symbols in
                Appendix C to this subpart, in conjunction with a description in the
                Feature section, to describe, for example, modified linkages, cross
                links and end caps, non-peptidyl bonds, etc., is embraced by this
                definition.
                 Note 1 to paragraph (a): Appendices A through F contain Tables
                1-6 of the World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009).
                * * * * *
                 (c) Patent applications that contain disclosures of nucleotide and/
                or amino acid sequences, as defined in paragraph (a) of this section,
                must contain a ``Sequence Listing'' as a separate part of the
                specification containing each of those nucleotide and/or amino acid
                sequences and associated information using the symbols and format in
                accordance with the requirements of Sec. Sec. 1.822 and 1.823. The
                ``Sequence Listing'' must be submitted as follows, except for a
                national stage entry under Sec. 1.495(b)(1), where the ``Sequence
                Listing'' has been previously communicated by the International Bureau
                or originally filed in the United States Patent and Trademark Office
                and complies with Patent Cooperation Treaty (PCT) Rule 5.2:
                 (1) As an ASCII plain text file, in compliance with Sec. 1.824,
                submitted via the USPTO patent electronic filing system or on a read-
                only optical disc under Sec. 1.52(e), accompanied by an incorporation
                by reference statement of the ASCII plain text file, in a separate
                paragraph of the specification, in accordance with Sec. 1.77(b)(5);
                 (2) As a PDF file via the USPTO patent electronic filing system; or
                 (3) On physical sheets of paper.
                 (d) Where the description or claims of a patent application discuss
                a sequence that is set forth in the ``Sequence Listing,'' in accordance
                with paragraph (c) of this section, reference must be made to the
                sequence by use of a sequence identifier (Sec. 1.823(a)(5)), preceded
                by ``SEQ ID NO:'' In the text of the description or claims, even if the
                sequence is also embedded in the text of the description or claims of
                the patent application. Where a sequence is presented in a drawing,
                reference must be made to the sequence by use of the sequence
                identifier (Sec. 1.823(a)(5)), either in the drawing or in the Brief
                Description of the Drawings, where the correlation between multiple
                sequences in the drawing and their sequence identifiers (Sec.
                1.823(a)(5)) in the Brief Description is clear.
                 (e)(1) If the ``Sequence Listing'' under paragraph (c) is submitted
                in an application filed under 35 U.S.C. 111(a) as a PDF file (Sec.
                1.821(c)(2)) via the USPTO patent electronic filing system or on
                physical sheets of paper (Sec. 1.821(c)(3)), then the following must
                be submitted:
                 (i) A CRF of the ``Sequence Listing,'' in accordance with the
                requirements of Sec. 1.824; and
                 (ii) A statement that the sequence information contained in the CRF
                submitted under paragraph (e)(1)(i) of this section is identical to the
                sequence information contained in the ``Sequence Listing'' under
                paragraph (c) of this section.
                 (2) If the ``Sequence Listing'' under paragraph (c) of this section
                in an application submitted under 35 U.S.C. 371 is a PDF file (Sec.
                1.821(c)(2)) or on physical sheets of paper (Sec. 1.821(c)(3)), and
                not also as an ASCII plain text file, in compliance with Sec. 1.824
                (Sec. 1.821(c)(1)), then the following must be submitted:
                 (i) A CRF of the ``Sequence Listing,'' in accordance with the
                requirements of Sec. 1.824; and
                 (ii) A statement that the sequence information contained in the CRF
                submitted under paragraph (e)(2)(i) of this section is identical to the
                sequence information contained in the ``Sequence Listing'' under
                paragraph (c)(2) or (3) of this section.
                [[Page 28315]]
                 (3) If a ``Sequence Listing'' in ASCII plain text format, in
                compliance with Sec. 1.824, has not been submitted for an
                international application under the PCT, and that application contains
                disclosures of nucleotide and/or amino acid sequences, as defined in
                paragraph (a) of this section, and is to be searched by the United
                States International Searching Authority or examined by the United
                States International Preliminary Examining Authority, then the
                following must be submitted:
                 (i) A CRF of the ``Sequence Listing,'' in accordance with the
                requirements of Sec. 1.824;
                 (ii) The late furnishing fee for providing a ``Sequence Listing''
                in response to an invitation, as set forth in Sec. 1.445(a)(5); and
                 (iii) A statement that the sequence information contained in the
                CRF, submitted under paragraph (e)(3)(i) of this section, does not go
                beyond the disclosure in the international application as filed, or a
                statement that the information recorded in the ASCII plain text file,
                submitted under paragraph (e)(3)(i) of this section, is identical to
                the sequence listing contained in the international application as
                filed, as applicable.
                 (4) The CRF may not be retained as a part of the patent application
                file.
                 (f) [Reserved]
                 (g) If any of the requirements of paragraphs (b) through (e) of
                this section are not satisfied at the time of filing under 35 U.S.C.
                111(a) or at the time of entering the national stage under 35 U.S.C.
                371, the applicant will be notified and given a period of time within
                which to comply with such requirements in order to prevent abandonment
                of the application. Any amendment to add or replace a ``Sequence
                Listing'' and CRF copy thereof in reply to a requirement under this
                paragraph must be submitted in accordance with the requirements of
                Sec. 1.825.
                 (h) If any of the requirements of paragraph (e)(3) of this section
                are not satisfied at the time of filing an international application
                under the PCT, and the application is to be searched by the United
                States International Searching Authority or examined by the United
                States International Preliminary Examining Authority, the applicant may
                be sent a notice necessitating compliance with the requirements within
                a prescribed time period. Where a ``Sequence Listing'' under PCT Rule
                13ter is provided in reply to a requirement under this paragraph, it
                must be accompanied by a statement that the information recorded in the
                ASCII plain text file under paragraph (e)(3)(i) of this section is
                identical to the sequence listing contained in the international
                application as filed, or does not go beyond the disclosure in the
                international application as filed, as applicable. It must also be
                accompanied by the late furnishing fee, as set forth in Sec.
                1.445(a)(5). If the applicant fails to timely provide the required CRF,
                the United States International Searching Authority shall search only
                to the extent that a meaningful search can be performed without the
                CRF, and the United States International Preliminary Examining
                Authority shall examine only to the extent that a meaningful
                examination can be performed without the CRF.
                0
                11. Amend Sec. 1.822 by revising paragraphs (b), (c)(1), (3), (5) and
                (6), (d)(1), (3) through (5), and (e) to read as follows:
                Sec. 1.822 Symbols and format to be used for nucleotide and/or amino
                acid sequence data.
                * * * * *
                 (b) The code for representing the nucleotide and/or amino acid
                sequence characters shall conform to the code set forth in Appendices A
                and C to this subpart. No code other than that specified in these
                sections shall be used in nucleotide and amino acid sequences. A
                modified base or modified or unusual amino acid may be presented in a
                given sequence as the corresponding unmodified base or amino acid if
                the modified base or modified or unusual amino acid is one of those
                listed in Appendices B and D to this subpart, and the modification is
                also set forth in the Feature section. Otherwise, each occurrence of a
                base or amino acid not appearing in Appendices A and C, shall be listed
                in a given sequence as ``n'' or ``Xaa,'' respectively, with further
                information, as appropriate, given in the Feature section, by including
                one or more feature keys listed in Appendices E and F to this subpart.
                 Note 1 to paragraph (b): Appendices A through F contain Tables
                1-6 of the World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009).
                 (c) * * *
                 (1) A nucleotide sequence shall be listed using the lowercase
                letter for representing the one-letter code for the nucleotide bases
                set forth in Appendix A to this subpart.
                * * * * *
                 (3) The bases in the coding parts of a nucleotide sequence shall be
                listed as triplets (codons). The amino acids corresponding to the
                codons in the coding parts of a nucleotide sequence shall be listed
                immediately below the corresponding codons. Where a codon spans an
                intron, the amino acid symbol shall be listed below the portion of the
                codon containing two nucleotides.
                * * * * *
                 (5) A nucleotide sequence shall be represented, only by a single
                strand, in the 5 to 3 direction, from left to right.
                 (6) The enumeration of nucleotide bases shall start at the first
                base of the sequence with number 1. The enumeration shall be continuous
                through the whole sequence in the direction 5 to 3. The enumeration
                shall appear in the right margin, next to the line containing the one-
                letter codes for the bases, and giving the number of the last base of
                that line.
                * * * * *
                 Note 2 to paragraph (c): Appendices A through F contain Tables
                1-6 of the World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009).
                 (d) * * *
                 (1) The amino acids in a protein or peptide sequence shall be
                listed using the three-letter abbreviation, with the first letter as an
                uppercase character, as in Appendix C to this subpart.
                * * * * *
                 (3) An amino acid sequence shall be represented in the amino to
                carboxy direction, from left to right, and the amino and carboxy groups
                shall not be represented in the sequence.
                 (4) The enumeration of amino acids may start at the first amino
                acid of the first mature protein, with the number 1. When represented,
                the amino acids preceding the mature protein (e.g., pre-sequences, pro-
                sequences, pre-pro-sequences and signal sequences) shall have negative
                numbers, counting backwards starting with the amino acid next to number
                1. Otherwise, the enumeration of amino acids shall start at the first
                amino acid at the amino terminal as number 1, and shall appear below
                every 5 amino acids of the sequence. The enumeration method for amino
                acid sequences that is set forth in this section remains applicable for
                amino acid sequences that are circular in configuration, with the
                exception that the designation of the first amino acid of the sequence
                may be made at the option of the applicant.
                 (5) An amino acid sequence that contains internal terminator
                symbols (e.g., ``Ter,'' ``*,'' or ``.,'' etc.) may not be
                [[Page 28316]]
                represented as a single amino acid sequence but shall be represented as
                separate amino acid sequences.
                 Note 3 to paragraph (d): Appendices A through F contain Tables
                1--6 of the World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009).
                 (e) A sequence with a gap or gaps shall be represented as a
                plurality of separate sequences, with separate sequence identifiers
                (Sec. 1.823(a)(5)), with the number of separate sequences being equal
                in number to the number of continuous strings of sequence data. A
                sequence composed of one or more noncontiguous segments of a larger
                sequence or segments from different sequences shall be presented as a
                separate sequence.
                0
                12. Revise Sec. 1.823 to read as follows:
                Sec. 1.823 Requirements for content of a ``Sequence Listing'' part of
                the specification.
                 (a) The ``Sequence Listing'' must comply with the following:
                 (1) The order and presentation of the items of information in the
                ``Sequence Listing'' shall conform to the arrangement in Appendix G.
                The submission of those items of information designated with an ``M''
                is mandatory. The submission of those items of information designated
                with an ``O'' is optional.
                 (2) Each item of information shall begin on a new line with the
                numeric identifier enclosed in angle brackets, as shown in Appendix G.
                 (3) Set forth numeric identifiers through at the
                beginning of the ``Sequence Listing.''
                 (4) Include each disclosed nucleotide and/or amino acid sequence,
                as defined in Sec. 1.821(a).
                 (5) Assign each sequence with a separate sequence identifier,
                beginning with 1 and increasing sequentially by integers, and include
                the sequence identifier in numeric identifier .
                 (6) Use the code ``000'' in place of the sequence where no sequence
                is present for a sequence identifier.
                 (7) Include the total number of SEQ ID NOs in numeric identifier
                , as defined in Appendix G, whether followed by a sequence or by
                the code ``000.''
                 (8) Must not contain more than 74 characters per line.
                 (b)(1) Unless paragraph (b)(2) of this section applies, if the
                ``Sequence Listing'' required by Sec. 1.821(c) is submitted as an
                ASCII plain text file via the USPTO patent electronic filing system or
                on a read-only optical disc, in compliance with Sec. 1.52(e), then the
                specification must contain a statement in a separate paragraph (see
                Sec. 1.77(b)(5)) that incorporates by reference the material in the
                ASCII plain text file identifying:
                 (i) The name of the file;
                 (ii) The date of creation; and
                 (iii) The size of the file in bytes.
                 (2) If the ``Sequence Listing'' required by Sec. 1.821(c) is
                submitted as an ASCII plain text file via the USPTO patent electronic
                filing system or on a read-only optical disc, in compliance with Sec.
                1.52(e) for an international application during the international
                stage, then incorporation by reference of the material in the ASCII
                plain text file is not required.
                 (3) A ``Sequence Listing'' required by Sec. 1.821(c) that is
                submitted as a PDF file (Sec. 1.821(c)(2)) via the USPTO patent
                electronic filing system or on physical sheets of paper (Sec.
                1.821(c)(3)), setting forth the nucleotide and/or amino acid sequence
                and associated information in accordance with paragraph (a) of this
                section:
                 (i) Must begin on a new page;
                 (ii) Must be titled ``Sequence Listing'';
                 (iii) Must not include material other than the ``Sequence Listing''
                itself;
                 (iv) Must have sheets containing no more than 66 lines, with each
                line containing no more than 74 characters;
                 (v) Should have sheets numbered independently of the numbering of
                the remainder of the application; and
                 (vi) Should use a fixed-width font exclusively throughout.
                0
                13. Revise Sec. 1.824 to read as follows:
                Sec. 1.824 Form and format for a nucleotide and/or amino acid
                sequence submission as an ASCII plain text file.
                 (a) A ``Sequence Listing'' under Sec. 1.821(c)(1) and the CRF
                required by Sec. 1.821(e) submitted as an ASCII plain text file may be
                created by any means, such as text editors, nucleotide/amino acid
                sequence editors, or other custom computer programs; however, the ASCII
                plain text file must conform to the following requirements:
                 (1) Must have the following compatibilities:
                 (i) Computer compatibility: PC or Mac[supreg];
                 (ii) Operating system compatibility: MS-DOS[supreg], MS-
                Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
                 (2) Must be in ASCII plain text, where:
                 (i) All printable characters (including the space character) are
                permitted;
                 (ii) No nonprintable (ASCII control) characters are permitted,
                except ASCII CRLF or LF as line terminators.
                 (3) Must be named as *.txt, where ``*'' is one character or a
                combination of characters limited to upper- or lowercase letters,
                numbers, hyphens, and underscores and does not exceed 60 characters in
                total, excluding the extension. No spaces or other types of characters
                are permitted in the file name.
                 (4) Must contain no more than 74 printable characters in each line.
                 (5) Pagination is not permitted; the ASCII plain text file must be
                one continuous file, with no ``hard page break'' codes and no page
                numbering.
                 (b) The ASCII plain text file must contain a copy of a single
                ``Sequence Listing'' in a single file and be submitted either:
                 (1) Electronically via the USPTO patent electronic filing system,
                where the file must not exceed 100 MB, and file compression is not
                permitted; or
                 (2) On read-only optical disc(s) in compliance with Sec. 1.52(e),
                where:
                 (i) A file that is not compressed must be contained on a single
                read-only optical disc;
                 (ii) The file may be compressed using WinZip[supreg], 7-Zip, or
                Unix[supreg]/Linux[supreg] Zip;
                 (iii) A compressed file must not be self-extracting; and
                 (iv) A compressed ASCII plain text file that does not fit on a
                single read-only optical disc may be split into multiple file parts, in
                accordance with the target read-only optical disc size, and labeled in
                compliance with 1.52(e)(5)(vi).
                0
                14. Revise Sec. 1.825 to read as follows:
                Sec. 1.825 Amendment to add or replace a ``Sequence Listing'' and CRF
                copy thereof.
                 (a) Any amendment adding a ``Sequence Listing'' (Sec. 1.821(c))
                after the application filing date must include:
                 (1) A ``Sequence Listing,'' in accordance with the requirements of
                Sec. Sec. 1.821 through 1.824, submitted as:
                 (i) An ASCII plain text file under Sec. 1.821(c)(1) via the USPTO
                patent electronic filing system or on a read-only optical disc, in
                compliance with Sec. 1.52(e);
                 (ii) PDF file via the USPTO patent electronic filing system; or
                 (iii) Physical sheets of paper;
                 (2) A request that the amendment be made:
                 (i) By incorporation by reference of the material in the ASCII
                plain text file, in a separate paragraph of the specification,
                identifying the name of the file, the date of creation, and the size of
                the file in bytes (see Sec. 1.77(b)(5)), for a ``Sequence Listing''
                submitted under Sec. 1.821(c)(1), except when submitted to the United
                States International Preliminary Examining Authority for an
                international application; or
                 (ii) By inserting, after the abstract of the disclosure, a
                ``Sequence Listing''
                [[Page 28317]]
                submitted as a PDF file under Sec. 1.821(c)(2) or submitted on
                physical sheets of paper under Sec. 1.821(c)(3), except when submitted
                to the United States International Preliminary Examining Authority for
                an international application;
                 (3) A statement that indicates the basis for the amendment, with
                specific references to particular parts of the application
                (specification, claims, drawings) for all sequence data in the
                ``Sequence Listing'' in the application as originally filed;
                 (4) A statement that the ``Sequence Listing'' includes no new
                matter;
                 (5) A new or substitute CRF under Sec. 1.821(e), if:
                 (i) The added ``Sequence Listing'' is submitted as a PDF file,
                under Sec. 1.821(c)(2), or on physical sheets of paper, under Sec.
                1.821(c)(3); and
                 (ii) A CRF, under Sec. 1.821(e), was not submitted, not compliant
                with Sec. 1.824, or not the same as the ``Sequence Listing''; and
                 (6) A statement that the sequence information contained in the CRF
                is the same as the sequence information contained in the added
                ``Sequence Listing,'' if submitted as a PDF file, under Sec.
                1.821(c)(2), or on physical sheets of paper, under Sec. 1.821(c)(3).
                 (b) Any amendment to a ``Sequence Listing'' (Sec. 1.821(c)) must
                include:
                 (1) A replacement ``Sequence Listing,'' in accordance with the
                requirements of Sec. Sec. 1.821 through 1.824, submitted as:
                 (i) An ASCII plain text file under Sec. 1.821(c)(1) via the USPTO
                patent electronic filing system, or on a read-only optical disc, in
                compliance with Sec. 1.52(e), labeled as ``REPLACEMENT MM/DD/YYYY''
                (with the month, day, and year of creation indicated);
                 (ii) A PDF file via the USPTO patent electronic filing system; or
                 (iii) Physical sheets of paper;
                 (2) A request that the amendment be made:
                 (i) By incorporation by reference of the material in the ASCII
                plain text file, in a separate paragraph of the specification
                (replacing any prior such paragraph, as applicable) identifying the
                name of the file, the date of creation, and the size of the file in
                bytes (see Sec. 1.77(b)(5)) for a ``Sequence Listing'' under Sec.
                1.821(c)(1), except when submitted to the United States International
                Preliminary Examining Authority for an international application; or
                 (ii) By placing, after the abstract of the disclosure, a ``Sequence
                Listing'' submitted as a PDF file, under Sec. 1.821(c)(2), or on
                physical sheets of paper, under Sec. 1.821(c)(3) (replacing any prior
                ``Sequence Listing,'' as applicable), except when submitted to the
                United States International Preliminary Examining Authority for an
                international application;
                 (3) A statement that identifies the location of all deletions,
                replacements, or additions to the ``Sequence Listing'';
                 (4) A statement that indicates the basis for the amendment, with
                specific references to particular parts of the application
                (specification, claims, drawings) as originally filed for all amended
                sequence data in the replacement ``Sequence Listing'';
                 (5) A statement that the replacement ``Sequence Listing'' includes
                no new matter;
                 (6) A new or substitute CRF under Sec. 1.821(e) with the amendment
                incorporated therein, if:
                 (i) The replacement ``Sequence Listing'' is submitted as a PDF
                file, under Sec. 1.821(c)(2), or on physical sheets of paper, under
                Sec. 1.821(c)(3); and
                 (ii) A CRF, under Sec. 1.821(e), was not submitted, not compliant
                with Sec. 1.824, or not the same as the submitted ``Sequence
                Listing''; and
                 (7) A statement that the sequence information contained in the CRF
                is the same as the sequence information contained in the replacement
                ``Sequence Listing'' when submitted as a PDF file, under Sec.
                1.821(c)(2), or on physical sheets of paper, under Sec. 1.821(c)(3).
                 (c) The specification of a complete application, filed on the
                application filing date, with a ``Sequence Listing'' as an ASCII plain
                text file, under Sec. 1.821(c)(1), without an incorporation by
                reference of the material contained in the ASCII plain text file, must
                be amended to contain a separate paragraph incorporating by reference
                the material contained in the ASCII plain text file, in accordance with
                Sec. 1.77(b)(5), except for international applications during the
                international stage or national stage.
                 (d) Any appropriate amendments to the ``Sequence Listing'' in a
                patent (e.g., by reason of reissue, reexamination, or certificate of
                correction) must comply with the requirements of paragraph (b) of this
                section.
                0
                15. Redesignate the appendix to subpart G of part 1 as appendix G, add
                appendices A through F, and revise newly redesignated appendix G as
                follows:
                Appendices A Through G of Subpart G of Part 1
                Appendix A: List of Nucleotides
                 Source: World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009)
                ------------------------------------------------------------------------
                 Origin of
                 Symbol Meaning designation
                ------------------------------------------------------------------------
                a............................... a................. adenine.
                g............................... g................. guanine.
                c............................... c................. cytosine.
                t............................... t................. thymine.
                u............................... u................. uracil.
                r............................... g or a............ purine
                y............................... t/u or c.......... pyrimidine.
                m............................... a or c............ amino.
                k............................... g or t/u.......... keto.
                s............................... g or c............ strong
                 interactions 3H-
                 bonds.
                w............................... a or t/u.......... weak interactions
                 2H-bonds.
                b............................... g or c or t/u..... not a.
                d............................... a or g or t/u..... not c.
                h............................... a or c or t/u..... not g.
                v............................... a or g or c....... not t, not u.
                n............................... a or g or c or t/ any
                 u, unknown, or
                 other.
                ------------------------------------------------------------------------
                [[Page 28318]]
                Appendix B: List of Modified Nucleotides
                 Source: World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009)
                ------------------------------------------------------------------------
                 Symbol Meaning
                ------------------------------------------------------------------------
                ac4c.............................. 4-acetylcytidine.
                chm5u............................. 5-(carboxyhydroxymethyl)uridine.
                cm................................ 2'-O-methylcytidine.
                cmnm5s2u.......................... 5-carboxymethylaminomethyl-2-
                 thiouridine.
                cmnm5u............................ 5-carboxymethylaminomethyluridine.
                d................................. dihydrouridine.
                fm................................ 2'-O-methylpseudouridine.
                gal q............................. beta, D-galactosylqueuosine.
                gm................................ 2'-O-methylguanosine.
                i................................. inosine.
                i6a............................... N6-isopentenyladenosine.
                m1a............................... 1-methyladenosine.
                m1f............................... 1-methylpseudouridine.
                m1g............................... 1-methylguanosine.
                m1i............................... 1-methylinosine.
                m22g.............................. 2,2-dimethylguanosine.
                m2a............................... 2-methyladenosine.
                m2g............................... 2-methylguanosine.
                m3c............................... 3-methylcytidine.
                m5c............................... 5-methylcytidine.
                m6a............................... N6-methyladenosine.
                m7g............................... 7-methylguanosine.
                mam5u............................. 5-methylaminomethyluridine.
                mam5s2u........................... 5-methoxyaminomethyl-2-thiouridine.
                man q............................. beta, D-mannosylqueuosine.
                mcm5s2u........................... 5-methoxycarbonylmethyl-2-
                 thiouridine.
                mcm5u............................. 5-methoxycarbonylmethyluridine.
                mo5u.............................. 5-methoxyuridine.
                ms2i6a............................ 2-methylthio-N6-
                 isopentenyladenosine.
                ms2t6a............................ N-((9-beta-D-ribofuranosyl-2-
                 methylthiopurine-6-
                 yl)carbamoyl)threonine.
                mt6a.............................. N-((9-beta-D-ribofuranosylpurine-6-
                 yl)N-methylcarbamoyl)threonine.
                mv................................ uridine-5-oxyacetic acid-
                 methylester.
                o5u............................... uridine-5-oxyacetic acid.
                osyw.............................. wybutoxosine.
                p................................. pseudouridine.
                q................................. queuosine.
                s2c............................... 2-thiocytidine.
                s2t............................... 5-methyl-2-thiouridine.
                s2u............................... 2-thiouridine.
                s4u............................... 4-thiouridine.
                t................................. 5-methyluridine.
                t6a............................... N-((9-beta-D-ribofuranosylpurine-6-
                 yl)-carbamoyl)threonine.
                tm................................ 2'-O-methyl-5-methyluridine.
                um................................ 2'-O-methyluridine.
                yw................................ wybutosine.
                x................................. 3-(3-amino-3-carboxy-propyl)uridine,
                 (acp3)u.
                ------------------------------------------------------------------------
                Appendix C: List of Amino Acids
                 Source: World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009)
                ------------------------------------------------------------------------
                 Symbol Meaning
                ------------------------------------------------------------------------
                Ala....................................... Alanine.
                Cys....................................... Cysteine.
                Asp....................................... Aspartic Acid.
                Glu....................................... Glutamic Acid.
                Phe....................................... Phenylalanine.
                Gly....................................... Glycine.
                His....................................... Histidine.
                Ile....................................... Isoleucine.
                Lys....................................... Lysine.
                Leu....................................... Leucine.
                Met....................................... Methionine.
                Asn....................................... Asparagine.
                Pro....................................... Proline.
                Gln....................................... Glutamine.
                Arg....................................... Arginine.
                Ser....................................... Serine.
                Thr....................................... Threonine.
                Val....................................... Valine.
                Trp....................................... Tryptophan.
                Tyr....................................... Tyrosine.
                Asx....................................... Asp or Asn.
                Glx....................................... Glu or Gln.
                Xaa....................................... unknown or other.
                ------------------------------------------------------------------------
                Appendix D: List of Modified and Unusual Amino Acids
                 Source: World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009)
                ------------------------------------------------------------------------
                 Symbol Meaning
                ------------------------------------------------------------------------
                Aad....................................... 2-Aminoadipic acid.
                bAad...................................... 3-Aminoadipic acid.
                bAla...................................... beta-Alanine, beta-
                 Aminopropionic acid.
                Abu....................................... 2-Aminobutyric acid.
                [[Page 28319]]
                
                4Abu...................................... 4-Aminobutyric acid,
                 piperidinic acid.
                Acp....................................... 6-Aminocaproic acid.
                Ahe....................................... 2-Aminoheptanoic acid.
                Aib....................................... 2-Aminoisobutyric acid.
                bAib...................................... 3-Aminoisobutyric acid.
                Apm....................................... 2-Aminopimelic acid.
                Dbu....................................... 2,4 Diaminobutyric acid.
                Des....................................... Desmosine.
                Dpm....................................... 2,2'-Diaminopimelic acid.
                Dpr....................................... 2,3-Diaminopropionic acid.
                EtGly..................................... N-Ethylglycine.
                EtAsn..................................... N-Ethylasparagine.
                Hyl....................................... Hydroxylysine.
                aHyl...................................... allo-Hydroxylysine.
                3Hyp...................................... 3-Hydroxyproline.
                4Hyp...................................... 4-Hydroxyproline.
                Ide....................................... Isodesmosine.
                aIle...................................... allo-Isoleucine.
                MeGly..................................... N-Methylglycine, sarcosine.
                MeIle..................................... N-Methylisoleucine.
                MeLys..................................... 6-N-Methyllysine.
                MeVal..................................... N-Methylvaline.
                Nva....................................... Norvaline.
                Nle....................................... Norleucine.
                Orn....................................... Ornithine.
                ------------------------------------------------------------------------
                Appendix E: List of Feature Keys Related to Nucleotide Sequences
                 Source: World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009)
                ------------------------------------------------------------------------
                 Key Description
                ------------------------------------------------------------------------
                allele....................... a related individual or strain contains
                 stable, alternative forms of the same
                 gene, which differs from the presented
                 sequence at this location (and perhaps
                 others).
                attenuator................... (1) region of DNA at which regulation of
                 termination of transcription occurs,
                 which controls the expression of some
                 bacterial operons; (2) sequence segment
                 located between the promoter and the
                 first structural gene that causes
                 partial termination of transcription.
                C_region..................... constant region of immunoglobulin light
                 and heavy chains, and T-cell receptor
                 alpha, beta, and gamma chains; includes
                 one or more exons depending on the
                 particular chain.
                CAAT_signal.................. CAAT box; part of a conserved sequence
                 located about 75 bp upstream of the
                 start point of eukaryotic transcription
                 units which may be involved in RNA
                 polymerase binding; consensus=GG (C or
                 T) CAATCT.
                CDS.......................... coding sequence; sequence of nucleotides
                 that corresponds with the sequence of
                 amino acids in a protein (location
                 includes stop codon); feature includes
                 amino acid conceptual translation.
                conflict..................... independent determinations of the
                 ``same'' sequence differ at this site or
                 region.
                D-loop....................... displacement loop; a region within
                 mitochondrial DNA in which a short
                 stretch of RNA is paired with one strand
                 of DNA, displacing the original partner
                 DNA strand in this region; also used to
                 describe the displacement of a region of
                 one strand of duplex DNA by a single
                 stranded invader in the reaction
                 catalyzed by RecA protein.
                D-segment.................... diversity segment of immunoglobulin heavy
                 chain, and T-cell receptor beta chain.
                enhancer..................... a cis-acting sequence that increases the
                 utilization of (some) eukaryotic
                 promoters, and can function in either
                 orientation and in any location
                 (upstream or downstream) relative to the
                 promoter.
                exon......................... region of genome that codes for portion
                 of spliced mRNA; may contain 5'UTR, all
                 CDSs, and 3'UTR.
                GC_signal.................... GC box; a conserved GC-rich region
                 located upstream of the start point of
                 eukaryotic transcription units which may
                 occur in multiple copies or in either
                 orientation; consensus=GGGCGG.
                gene......................... region of biological interest identified
                 as a gene and for which a name has been
                 assigned.
                iDNA......................... intervening DNA; DNA which is eliminated
                 through any of several kinds of
                 recombination.
                intron....................... a segment of DNA that is transcribed, but
                 removed from within the transcript by
                 splicing together the sequences (exons)
                 on either side of it.
                J_segment.................... joining segment of immunoglobulin light
                 and heavy chains, and T-cell receptor
                 alpha, beta, and gamma chains.
                LTR.......................... long terminal repeat, a sequence directly
                 repeated at both ends of a defined
                 sequence, of the sort typically found in
                 retroviruses.
                mat_peptide.................. mature peptide or protein coding
                 sequence; coding sequence for the mature
                 or final peptide or protein product
                 following post-translational
                 modification; the location does not
                 include the stop codon (unlike the
                 corresponding CDS).
                misc_binding................. site in nucleic acid which covalently or
                 non-covalently binds another moiety that
                 cannot be described by any other Binding
                 key (primer_bind or protein_bind).
                misc_difference.............. feature sequence is different from that
                 presented in the entry and cannot be
                 described by any other Difference key
                 (conflict, unsure, old_sequence,
                 mutation, variation, allele, or
                 modified_base).
                misc_feature................. region of biological interest which
                 cannot be described by any other feature
                 key; a new or rare feature.
                misc_recomb.................. site of any generalized, site-specific or
                 replicative recombination event where
                 there is a breakage and reunion of
                 duplex DNA that cannot be described by
                 other recombination keys (iDNA and
                 virion) or qualifiers of source key (/
                 insertion_seq, /transposon, /proviral).
                misc_RNA..................... any transcript or RNA product that cannot
                 be defined by other RNA keys
                 (prim_transcript, precursor_RNA, mRNA,
                 5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS,
                 sig_peptide, transit_peptide,
                 mat_peptide, intron, polyA_site, rRNA,
                 tRNA, scRNA, and snRNA).
                misc_signal.................. any region containing a signal
                 controlling or altering gene function or
                 expression that cannot be described by
                 other Signal keys (promoter,
                 CAAT_signal, TATA_signal, -35_signal, -
                 10_signal, GC_signal, RBS, polyA_signal,
                 enhancer, attenuator, terminator, and
                 rep_origin).
                misc_structure............... any secondary or tertiary structure or
                 conformation that cannot be described by
                 other Structure keys (stem_loop and D-
                 loop).
                modified_base................ the indicated nucleotide is a modified
                 nucleotide and should be substituted for
                 by the indicated molecule (given in the
                 mod_base qualifier value).
                mRNA......................... messenger RNA; includes 5' untranslated
                 region (5'UTR), coding sequences (CDS,
                 exon) and 3' untranslated region
                 (3'UTR).
                mutation..................... a related strain has an abrupt,
                 inheritable change in the sequence at
                 this location.
                N_region..................... extra nucleotides inserted between
                 rearranged immunoglobulin segments.
                old_sequence................. the presented sequence revises a previous
                 version of the sequence at this
                 location.
                polyA_signal................. recognition region necessary for
                 endonuclease cleavage of an RNA
                 transcript that is followed by
                 polyadenylation; consensus=AATAAA.
                polyA_site................... site on an RNA transcript to which will
                 be added adenine residues by post-
                 transcriptional polyadenylation.
                [[Page 28320]]
                
                precursor_RNA................ any RNA species that is not yet the
                 mature RNA product; may include 5'
                 clipped region (5'clip), 5' untranslated
                 region (5'UTR), coding sequences (CDS,
                 exon), intervening sequences (intron),
                 3' untranslated region (3'UTR), and 3'
                 clipped region (3'clip).
                prim_transcript.............. primary (initial, unprocessed)
                 transcript; includes 5' clipped region
                 (5'clip), 5' untranslated region
                 (5'UTR), coding sequences (CDS, exon),
                 intervening sequences (intron), 3'
                 untranslated region (3'UTR), and 3'
                 clipped region (3'clip).
                primer_bind.................. non-covalent primer binding site for
                 initiation of replication,
                 transcription, or reverse transcription;
                 includes site(s) for synthetic, for
                 example, PCR primer elements.
                promoter..................... region on a DNA molecule involved in RNA
                 polymerase binding to initiate
                 transcription.
                protein_bind................. non-covalent protein binding site on
                 nucleic acid.
                RBS.......................... ribosome binding site.
                repeat_region................ region of genome containing repeating
                 units.
                repeat_unit.................. single repeat element.
                rep_origin................... origin of replication; starting site for
                 duplication of nucleic acid to give two
                 identical copies.
                rRNA......................... mature ribosomal RNA; the RNA component
                 of the ribonucleoprotein particle
                 (ribosome) which assembles amino acids
                 into proteins.
                S_region..................... switch region of immunoglobulin heavy
                 chains; involved in the rearrangement of
                 heavy chain DNA leading to the
                 expression of a different immunoglobulin
                 class from the same B-cell.
                satellite.................... many tandem repeats (identical or
                 related) of a short basic repeating
                 unit; many have a base composition or
                 other property different from the genome
                 average that allows them to be separated
                 from the bulk (main band) genomic DNA.
                scRNA........................ small cytoplasmic RNA; any one of several
                 small cytoplasmic RNA molecules present
                 in the cytoplasm and (sometimes) nucleus
                 of a eukaryote.
                sig_peptide.................. signal peptide coding sequence; coding
                 sequence for an N-terminal domain of a
                 secreted protein; this domain is
                 involved in attaching nascent
                 polypeptide to the membrane; leader
                 sequence.
                snRNA........................ small nuclear RNA; any one of many small
                 RNA species confined to the nucleus;
                 several of the snRNAs are involved in
                 splicing or other RNA processing
                 reactions.
                source....................... identifies the biological source of the
                 specified span of the sequence; this key
                 is mandatory; every entry will have, as
                 a minimum, a single source key spanning
                 the entire sequence; more than one
                 source key per sequence is permissible.
                stem_loop.................... hairpin; a double-helical region formed
                 by base-pairing between adjacent
                 (inverted) complementary sequences in a
                 single strand of RNA or DNA.
                STS.......................... Sequence Tagged Site; short, single-copy
                 DNA sequence that characterizes a
                 mapping landmark on the genome and can
                 be detected by PCR; a region of the
                 genome can be mapped by determining the
                 order of a series of STSs.
                TATA_signal.................. TATA box; Goldberg-Hogness box; a
                 conserved AT-rich septamer found about
                 25 bp before the start point of each
                 eukaryotic RNA polymerase II transcript
                 unit which may be involved in
                 positioning the enzyme for correct
                 initiation; consensus=TATA(A or T)A(A or
                 T).
                terminator................... sequence of DNA located either at the end
                 of the transcript or adjacent to a
                 promoter region that causes RNA
                 polymerase to terminate transcription;
                 may also be site of binding of repressor
                 protein.
                transit_peptide.............. transit peptide coding sequence; coding
                 sequence for an N-terminal domain of a
                 nuclear-encoded organellar protein; this
                 domain is involved in post-translational
                 import of the protein into the
                 organelle.
                tRNA......................... mature transfer RNA, a small RNA molecule
                 (75-85 bases long) that mediates the
                 translation of a nucleic acid sequence
                 into an amino acid sequence.
                unsure....................... author is unsure of exact sequence in
                 this region.
                V_region..................... variable region of immunoglobulin light
                 and heavy chains, and T-cell receptor
                 alpha, beta, and gamma chains; codes for
                 the variable amino terminal portion; can
                 be made up from V_segments, D_segments,
                 N_regions, and J_segments.
                V_segment.................... variable segment of immunoglobulin light
                 and heavy chains, and T-cell receptor
                 alpha, beta, and gamma chains; codes for
                 most of the variable region (V_region)
                 and the last few amino acids of the
                 leader peptide.
                variation.................... a related strain contains stable
                 mutations from the same gene (for
                 example, RFLPs, polymorphisms, etc.)
                 which differ from the presented sequence
                 at this location (and possibly others).
                3'clip....................... 3'-most region of a precursor transcript
                 that is clipped off during processing.
                3'UTR........................ region at the 3' end of a mature
                 transcript (following the stop codon)
                 that is not translated into a protein.
                5'clip....................... 5'-most region of a precursor transcript
                 that is clipped off during processing.
                5'UTR........................ region at the 5' end of a mature
                 transcript (preceding the initiation
                 codon) that is not translated into a
                 protein.
                -10_signal................... pribnow box; a conserved region about 10
                 bp upstream of the start point of
                 bacterial transcription units which may
                 be involved in binding RNA polymerase;
                 consensus=TAtAaT.
                -35_signal................... a conserved hexamer about 35 bp upstream
                 of the start point of bacterial
                 transcription units; consensus=TTGACa [
                 ] or TGTTGACA [ ].
                ------------------------------------------------------------------------
                Appendix F: List of Feature Keys Related to Protein Sequences
                 Source: World Intellectual Property Organization (WIPO) Handbook
                on Industrial Property Information and Documentation, Standard
                ST.25: Standard for the Presentation of Nucleotide and Amino Acid
                Sequence Listings in Patent Applications (2009)
                ------------------------------------------------------------------------
                 Key Description
                ------------------------------------------------------------------------
                CONFLICT.......................... different papers report differing
                 sequences.
                VARIANT........................... authors report that sequence
                 variants exist.
                VARSPLIC.......................... description of sequence variants
                 produced by alternative splicing.
                [[Page 28321]]
                
                MUTAGEN........................... site which has been experimentally
                 altered.
                MOD_RES........................... post-translational modification of a
                 residue.
                ACETYLATION....................... N-terminal or other.
                AMIDATION......................... generally at the C-terminal of a
                 mature active peptide.
                BLOCKED........................... undetermined N- or C-terminal
                 blocking group.
                FORMYLATION....................... of the N-terminal methionine.
                GAMMA-CARBOXYGLUTAMIC ACID of asparagine, aspartic acid,
                 HYDROXYLATION. proline, or lysine.
                METHYLATION....................... generally of lysine or arginine.
                PHOSPHORYLATION................... of serine, threonine, tyrosine,
                 aspartic acid or histidine.
                PYRROLIDONE CARBOXYLIC ACID....... N-terminal glutamate which has
                 formed an internal cyclic lactam.
                SULFATATION....................... generally of tyrosine.
                LIPID............................. covalent binding of a lipidic
                 moiety.
                MYRISTATE......................... myristate group attached through an
                 amide bond to the N-terminal
                 glycine residue of the mature form
                 of a protein or to an internal
                 lysine residue.
                PALMITATE......................... palmitate group attached through a
                 thioether bond to a cysteine
                 residue or through an ester bond to
                 a serine or threonine residue.
                FARNESYL.......................... farnesyl group attached through a
                 thioether bond to a cysteine
                 residue.
                GERANYL-GERANYL................... geranyl-geranyl group attached
                 through a thioether bond to a
                 cysteine residue.
                GPI-ANCHOR........................ glycosyl-phosphatidylinositol (GPI)
                 group linked to the alpha-carboxyl
                 group of the C-terminal residue of
                 the mature form of a protein.
                N-ACYL DIGLYCERIDE................ N-terminal cysteine of the mature
                 form of a prokaryotic lipoprotein
                 with an amide-linked fatty acid and
                 a glyceryl group to which two fatty
                 acids are linked by ester linkages.
                DISULFID.......................... disulfide bond; the `FROM' and `TO'
                 endpoints represent the two
                 residues which are linked by an
                 intra-chain disulfide bond; if the
                 `FROM' and `TO' endpoints are
                 identical, the disulfide bond is an
                 interchain one and the description
                 field indicates the nature of the
                 cross-link.
                THIOLEST.......................... thiolester bond; the `FROM' and `TO'
                 endpoints represent the two
                 residues which are linked by the
                 thiolester bond.
                THIOETH........................... thioether bond; the `FROM' and `TO'
                 endpoints represent the two
                 residues which are linked by the
                 thioether bond.
                CARBOHYD.......................... glycosylation site; the nature of
                 the carbohydrate (if known) is
                 given in the description field.
                METAL............................. binding site for a metal ion; the
                 description field indicates the
                 nature of the metal.
                BINDING........................... binding site for any chemical group
                 (co-enzyme, prosthetic group,
                 etc.); the chemical nature of the
                 group is given in the description
                 field.
                SIGNAL............................ extent of a signal sequence
                 (prepeptide).
                TRANSIT........................... extent of a transit peptide
                 (mitochondrial, chloroplastic, or
                 for a microbody).
                PROPEP............................ extent of a propeptide.
                CHAIN............................. extent of a polypeptide chain in the
                 mature protein.
                PEPTIDE........................... extent of a released active peptide.
                DOMAIN............................ extent of a domain of interest on
                 the sequence; the nature of that
                 domain is given in the description
                 field.
                CA_BIND........................... extent of a calcium-binding region.
                DNA_BIND.......................... extent of a DNA-binding region.
                NP_BIND........................... extent of a nucleotide phosphate
                 binding region; the nature of the
                 nucleotide phosphate is indicated
                 in the description field.
                TRANSMEM.......................... extent of a transmembrane region.
                ZN_FING........................... extent of a zinc finger region.
                SIMILAR........................... extent of a similarity with another
                 protein sequence; precise
                 information, relative to that
                 sequence, is given in the
                 description field.
                REPEAT............................ extent of an internal sequence
                 repetition.
                HELIX............................. secondary structure: Helices, for
                 example, Alpha-helix, 3(10) helix,
                 or Pi-helix.
                STRAND............................ secondary structure: Beta-strand,
                 for example, Hydrogen bonded beta-
                 strand, or Residue in an isolated
                 beta-bridge.
                TURN.............................. secondary structure Turns, for
                 example, H-bonded turn (3-turn, 4-
                 turn, or 5-turn).
                ACT_SITE.......................... amino acid(s) involved in the
                 activity of an enzyme.
                SITE.............................. any other interesting site on the
                 sequence.
                INIT_MET.......................... the sequence is known to start with
                 an initiator methionine.
                NON_TER........................... the residue at an extremity of the
                 sequence is not the terminal
                 residue; if applied to position 1,
                 this signifies that the first
                 position is not the N-terminus of
                 the complete molecule; if applied
                 to the last position, it signifies
                 that this position is not the C-
                 terminus of the complete molecule;
                 there is no description field for
                 this key.
                NON_CONS.......................... non consecutive residues; indicates
                 that two residues in a sequence are
                 not consecutive and that there are
                 a number of unsequenced residues
                 between them.
                UNSURE............................ uncertainties in the sequence; used
                 to describe region(s) of a sequence
                 for which the authors are unsure
                 about the sequence assignment.
                ------------------------------------------------------------------------
                [[Page 28322]]
                Appendix G: Numeric Identifiers
                ----------------------------------------------------------------------------------------------------------------
                 Mandatory (M) or
                 Numeric identifier Definition Comments and format optional (O)
                ----------------------------------------------------------------------------------------------------------------
                ................................ Applicant.............. If Applicant is M.
                 inventor, then
                 preferably max. of 10
                 names; one name per
                 line; preferable
                 format: Surname, Other
                 Names and/or Initials.
                ................................ Title of Invention..... ....................... M.
                ................................ File Reference......... Personal file reference M when filed prior to
                 assignment or appl.
                 number.
                ................................ Current Application Specify as: US 09/ M, if available.
                 Number. 999,999 or PCT/US09/
                 99999.
                ................................ Current Filing Date.... Specify as: yyyy-mm-dd. M, if available.
                ................................ Prior Application Specify as: US 09/ M, if applicable
                 Number. 999,999 or PCT/US09/ include priority
                 99999. documents under 35
                 U.S.C. 119 and 120.
                ................................ Prior Application Specify as: yyyy-mm-dd. M, if applicable.
                 Filing Date.
                ................................ Number of SEQ ID NOs... Count includes total M.
                 number of SEQ ID NOs.
                ................................ Software............... Name of software used O.
                 to create the
                 ``Sequence Listing.''.
                ................................ SEQ ID NO:#:........... Response shall be an M.
                 integer representing
                 the SEQ ID NO shown.
                ................................ Length................. Respond with an integer M.
                 expressing the number
                 of bases or amino acid
                 residues.
                ................................ Type................... Whether presented M.
                 sequence molecule is
                 DNA, RNA, or PRT
                 (protein). If a
                 nucleotide sequence
                 contains both DNA and
                 RNA fragments, the
                 type shall be ``DNA.''
                 In addition, the
                 combined DNA/RNA
                 molecule shall be
                 further described in
                 the to
                 feature section.
                ................................ Organism............... Scientific name, i.e. M.
                 Genus/species, Unknown
                 or Artificial
                 Sequence. In addition,
                 the ``Unknown'' or
                 ``Artificial
                 Sequence'' organisms
                 shall be further
                 described in the
                 to feature
                 section.
                ................................ Feature................ Leave blank after M, under the following
                 . conditions: if ``n,''
                 provide for a ``Xaa,'' or a modified
                 description of points or unusual L-amino
                 of biological acid or modified base
                 significance in the was used in a
                 sequence. sequence; if ORGANISM
                 is ``Artificial
                 Sequence'' or
                 ``Unknown''; if
                 molecule is combined
                 DNA/RNA.
                ................................ Name/Key............... Provide appropriate M, under the following
                 identifier for conditions: if ``n,''
                 feature, from WIPO ``Xaa,'' or a modified
                 Standard ST.25 (2009), or unusual L-amino
                 Appendices E and F to acid or modified base
                 this subpart. was used in a
                 sequence.
                ................................ Location............... Specify location within M, under the following
                 sequence; where conditions: if ``n,''
                 appropriate, state ``Xaa,'' or a modified
                 number of first and or unusual L-amino
                 last bases/amino acids acid or modified base
                 in feature. was used in a
                 sequence.
                ................................ Other Information...... Other relevant M, under the following
                 information; four conditions: if ``n,''
                 lines maximum. ``Xaa,'' or a modified
                 or unusual L-amino
                 acid or modified base
                 was used in a
                 sequence; if ORGANISM
                 is ``Artificial
                 Sequence'' or
                 ``Unknown''; if
                 molecule is combined
                 DNA/RNA.
                ................................ Publication Information Leave blank after O.
                ................................ Authors................ Preferably max. of 10 O.
                 named authors of
                 publication; specify
                 one name per line;
                 preferable format:
                 Surname, Other Names
                 and/or Initials.
                ................................ Title.................. ....................... O.
                ................................ Journal................ ....................... O.
                ................................ Volume................. ....................... O.
                ................................ Issue.................. ....................... O.
                ................................ Pages.................. ....................... O.
                ................................ Date................... Journal date on which O.
                 data published;
                 specify as yyyy-mm-dd,
                 MMM-yyyy or Season-
                 yyyy.
                ................................ Database Accession Accession number O.
                 Number. assigned by database,
                 including database
                 name.
                ................................ Database Entry Date.... Date of entry in O.
                 database; specify as
                 yyyy-mm-dd or MMM-yyyy.
                ................................ Patent Document Number. Document number; for O.
                 patent-type citations
                 only. Specify as, for
                 example, US 09/999,999.
                ................................ Patent Filing Date..... Document filing date, O.
                 for patent-type
                 citations only;
                 specify as yyyy-mm-dd.
                [[Page 28323]]
                
                ................................ Publication Date....... Document publication O.
                 date, for patent-type
                 citations only;
                 specify as yyyy-mm-dd.
                ................................ Relevant Residues...... FROM (position) TO O.
                 (position).
                ................................ Sequence............... SEQ ID NO should follow M.
                 the numeric identifier
                 and should appear on
                 the line preceding the
                 actual sequence.
                ----------------------------------------------------------------------------------------------------------------
                Andrew Hirshfeld,
                Commissioner for Patents, Performing the Functions and Duties of the
                Under Secretary of Commerce for Intellectual Property and Director of
                the United States Patent and Trademark Office.
                [FR Doc. 2021-10421 Filed 5-25-21; 8:45 am]
                BILLING CODE 3510-16-P
                

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