Electronic Submission of a Sequence Listing, a Large Table, or a Computer Program Listing Appendix in Patent Applications
| Citation | 86 FR 57035 |
| Record Number | 2021-22217 |
| Published date | 14 October 2021 |
| Section | Rules and Regulations |
| Court | Patent And Trademark Office |
Federal Register, Volume 86 Issue 196 (Thursday, October 14, 2021)
[Federal Register Volume 86, Number 196 (Thursday, October 14, 2021)]
[Rules and Regulations]
[Pages 57035-57058]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2021-22217]
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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: Final rule.
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SUMMARY: The United States Patent and Trademark Office (USPTO or
Office) is amending 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) plain 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,
submission of large data submission in ASCII plain text format can be
made on physical media. To that end, the rules of practice are amended
to provide applicants with the ability to use physical media larger
than compact discs (CDs) for submission of data in ASCII plain text
format, such as an electronic version of amino acid and nucleotide
sequence information, information compiled in a large table, or
[[Page 57036]]
information related to a computer program listing. Additionally,
extraction of compressed data files, which had not been permitted in
the past for certain submissions, will be permitted if the compressed
data files are compliant with the requirements of the rules. Other
rules related to certain obsolete and non-secure methods of presenting
data are eliminated.
DATES: This rule is effective on November 15, 2021.
FOR FURTHER INFORMATION CONTACT: Mary C. Till, Senior Legal Advisor,
Office of Patent Legal Administration, Office of the Deputy
Commissioner for Patents, at [email protected]; or Ali Salimi, Senior
Legal Advisor, Office of Patent Legal Administration, Office of the
Deputy Commissioner for Patents, at [email protected].
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 system, this rulemaking
expands the types of physical media that can be used for such a
submission to include read-only optical discs. 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 related to biotechnology
inventions, the rules of practice no longer permit an applicant to rely
on a previously submitted computer readable form (CRF) of required
sequence information. The 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 rules will also permit an ASCII plain text file
(.txt) 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
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 plain text files. The 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'' incorporate the requirements and conditions for such
submissions set forth in the Legal Framework for Patent Electronic
System into the rules of practice for filing such documents in
electronic form and expand the types of physical media acceptable for
submissions that exceed the USPTO patent electronic filing system
limits. The changes do not alter the requirements and conditions set
forth in the Legal Framework for Patent Electronic System.
Submission of ASCII plain text files: 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. However, due to the
limited storage capacity of compact discs, the USPTO is revising the
rules to permit the use of Digital Video Disc-Recordable (DVD-R or
DVD+R) as an alternative to a compact disc. 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 if the applicant has not filed a ``Sequence
Listing'' in a Portable Document Format (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 procedure is expressly
incorporated into these 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 on 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'' must be submitted on read-only optical discs.
Submission of a ``Sequence Listing'' as an ASCII plain 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. Prior to this rulemaking, such files could not be
compressed; thus, necessitating the use of multiple CD-ROMs or CD-Rs.
The 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
[[Page 57037]]
can fit on a single disc with the data integrity remaining intact.
Prior to this rulemaking, the rules of practice (37 CFR 1.52(e),
1.96(c), and 1.824) recited the use of certain obsolete computer and
operating system formats. Updated computer and operating system formats
are now added, and references to obsolete media are eliminated. Changes
to 37 CFR 1.58 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, 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 related to
the arrangement of the specification 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, may 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 plain text 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 present
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.
Submission of data related to disclosures of amino acids and/or
nucleotides: 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 submission of such data referred
to as a ``Sequence Listing'' and a CRF of the ``Sequence Listing.''
Prior to this rulemaking, a ``Sequence Listing'' exceeding the USPTO
patent electronic filing system submission limit had to be submitted
with a total of three disc copies to the USPTO to comply with the
``Sequence Listing'' regulation requirements. The three disc copies
included (1) a first disc copy of the 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 present rule changes permit that a single
read-only optical disc copy of a ``Sequence Listing'' as an ASCII plain
text file can be submitted, and that such submission will 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, will
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 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.
----------------------------------------------------------------------------------------------------------------
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 via Listing'' in reference of the
the USPTO patent physical paper ASCII plain text
electronic filing copies or file into the
system, complies submitted via the specification
with both 37 CFR USPTO patent (see MPEP 502.05).
1.821(c) and electronic filing
1.821(e), no system as a PDF
separate CRF image file and a
needed. CRF on a read-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 plain text
optical disc in a copies and a CRF file into the
single copy, the on a read-only specification (37
single copy optical disc along CFR 1.52(e)(8) as
complies with both with a statement added in these
37 CFR 1.821(c) that the CRF and rules).
and 1.821(e), no the physical paper
separate CRF submission are the
needed. 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 $1,060
a read-only physical paper ASCII plain text for an
optical disc in a copies and a CRF file into the undiscounted
single copy, the on a read-only specification (37 entity, $530 for
single copy optical disc along CFR 1.52(e)(8) as a small entity,
complies with both with a statement added in these and $265 for a
37 CFR 1.821(c) that the CRF and rules). micro entity.
and 1.821(e), no the physical paper
separate CRF submission are the
needed. same.
[[Page 57038]]
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 $10,500
a read-only physical paper ASCII plain text for an
optical disc in a copies and a CRF file into the undiscounted
single copy, the on a read-only specification (37 entity, $5,250
single copy optical disc along CFR 1.52(e)(8) as for a small
complies with both with a statement added in these entity, and
37 CFR 1.821(c) that the CRF and rules). $2,625 for a
and 1.821(e), no the physical paper micro entity.
separate CRF submission are the
needed. Should 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.
----------------------------------------------------------------------------------------------------------------
Prior to this rulemaking, the rules of practice related to the
form, content, and submission requirements of ``Sequence Listings''
complied with World Intellectual Property Organization (WIPO) Standard
ST.25. The rule changes and modifications in this document 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
rules prior to this rulemaking, the present changes continue to permit
the submission of a ``Sequence Listing'' on physical sheets of paper or
as a PDF image file. Furthermore, like the previous rules, the present
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 will 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 will 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)(1)(ii)
and 1.821(e)(2)(ii), that the CRF is identical to either the PDF or the
physical paper version of the ``Sequence Listing'' is required.
The rule changes no longer permit the transfer of a CRF from a
parent or related application to another application. In light of the
ability to download a ``Sequence Listing'' from granted U.S. patents
and U.S. patent application publications via Public Patent Application
Information Retrieval (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
changes to the rules of practice eliminate the practice of CRF
transfers.
As noted earlier, the present changes will continue to permit the
submission of a ``Sequence Listing'' on physical sheets of paper or as
a PDF image file. However, WIPO Standard ST.26 is currently scheduled
to take effect on January 1, 2022, and will replace WIPO Standard
ST.25. WIPO Standard ST.26 will require that a ``Sequence Listing''
must be presented as a single file in eXtensible Markup Language (XML).
Presentation in XML file format cannot be accomplished on paper or as a
PDF image file. As a result, in an original application filed on or
after WIPO Standard ST.26 takes effect (currently scheduled to happen
on January 1, 2022), the ``Sequence Listing'' part will not be accepted
on physical sheets of paper or as a PDF image file. To prepare for the
changes under WIPO Standard ST.26, the USPTO is revising the rules of
practice to facilitate ``Sequence Listing'' submissions by permitting a
single ASCII plain text file submission to both meet the ``Sequence
Listing'' requirement and serve as the CRF of the ``Sequence Listing.''
That is, under these rule changes, a single ASCII plain text file
submission of a ``Sequence Listing'' will comply with both 37 CFR
1.821(c) and (e).
Prior to this rulemaking, 37 CFR 1.821(a) incorporated 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,
the present rulemaking adds these tables as Appendices A-F of subpart G
of part 1 (explicitly incorporating the text of the WIPO tables into
the CFR). Prior to this rulemaking, 37 CFR 1.823(b) also included a
table containing all numeric identifiers. To improve the readability of
the regulations, this table is 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)
[[Page 57039]]
were exempted from these general requirements (37 CFR 1.121(b)) prior
to this rulemaking. The present 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 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 the 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
The following is a discussion of the amendments to 37 CFR part 1.
Section 1.52
The heading of Sec. 1.52 is revised to read: Language, paper,
writing, margins, read-only optical disc specifications.
Section 1.52(e) is amended to reference electronic documents
``submitted on a read-only optical disc,'' with additional conforming
changes made throughout. Since Sec. 1.52(e) only governs electronic
documents submitted on discs, in particular, 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 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 revised to indicate that ``Large Tables,'' as
described in 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 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 DVD-R or DVD+R (Sec. 1.52(e)(2)(ii)).
Section 1.52(e)(3) is 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 changes to the rules of practice indicate that the use
of ASCII plain text is required when submitting files on physical media
(Sec. 1.52(e)(3)(iii)). The changes 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 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 amended to provide for
such duplicate copies. Duplicate copies for ``Large Tables'' and a
``Computer Program Listing Appendix'' will 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 revised 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 revised to enumerate the labeling
requirements for 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 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 will 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 Office file wrapper,
and reviewing the ASCII plain text file. A first copy of the read-only
optical disc 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 present
rule change requires the submission of a single read-only optical disc.
Once the ``Sequence Listing'' is loaded into the USPTO's Supplemental
Complex Repository for Examiners 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 revised to state that any amendment to the
information on a read-only optical disc must be made in accordance with
specified provisions, 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 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 added to indicate that should a file be
unreadable, then the USPTO will treat the submission as
[[Page 57040]]
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, the OPAP will issue a notice
indicating that the file is unreadable, and a replacement will be
required.
Section 1.52(f) is 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 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 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 to also 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 added to provide a cross-reference to
existing Sec. 1.21(o), which sets forth a surcharge for the 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. This means that a
``Sequence Listing'' submitted in electronic form on read-only optical
discs, in compliance with either Sec. Sec. 1.821(c) 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, a surcharge
under Sec. 1.21(o)(2) will be imposed.
Section 1.58
Section 1.58(b) is revised 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 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.
Section 1.58(d) is 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 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 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 added to provide the procedure that will 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 will be necessary. An
updated incorporation by reference statement will be required, along
with the necessary statement regarding any deletions, replacements, or
additions to the ASCII plain text file. Additionally, a statement that
the replacement ASCII plain text file contains no new matter will also
be required.
Section 1.58(h) is added to specify that should ``Large Tables'' be
submitted as an ASCII plain text file on the application filing date,
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 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 disc
copies that are not identical to each other. Two discs would be
considered not identical when, e.g., the files contained on those discs
are not the same. 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 added to require that any amendment to the
information on a read-only optical disc must be by way of duplicate
replacement read-only optical discs, 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 disc copies that
are not identical to each other. Two discs would be considered not
identical when, e.g., the files contained on those discs are not the
same.
Section 1.71
Section 1.71(f) is 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 as a PDF image file
via the USPTO patent electronic filing system. In such cases where
there is a ``Sequence Listing'' and a separate CRF of the ``Sequence
Listing,'' the ``Sequence Listing'' must be on a separate sheet(s).
[[Page 57041]]
Section 1.77
Section 1.77(b)(5) is revised to clarify when an incorporation by
reference statement is needed. The rule change allows 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. 1.96(c), Sec. 1.821(c), or
Sec. 1.58(c), respectively. The incorporation by reference statement
must 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 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, should follow the other sections of the
specification.
Section 1.96
Section 1.96(a) is revised to replace ``printout'' with
``document.''
Section 1.96(c) is 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). 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 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 added to state requirements (i) through (iv)
for amendments to delete, replace, or add to the information in a
``Computer Program Listing Appendix'' submitted in electronic form in
ASCII plain text.
Section 1.96(c)(6) is 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 related 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 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 section indicates how the
USPTO will treat the submission of the two read-only optical disc
copies should they not be identical. Two discs would be considered not
identical when, e.g., the files contained on those discs are not the
same.
Section 1.121
Section 1.121(b) is revised, and Sec. 1.121(b)(6) is 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 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
than 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 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 the current Sec. 1.173(b)(1) stating
that the paragraph is not applicable to discs is not included in the
new Sec. 1.173(b)(1)(i).
Section 1.173(b)(1)(ii) is 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 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 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 `U' and end with `U' to properly identify the material being
added.''
Section 1.530
The heading of Sec. 1.530(d)(1) is 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)), and a ``Sequence Listing'' (Sec. 1.821(c)) are made in a
different manner than changes to the other parts of the specification.
The manner of making changes to the specification, other than to
the claims, is moved from Sec. 1.530(d)(1) 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 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 revised to remove all prior references to WIPO
Standard ST.25 (1998) and instead cross-reference new Appendices A
through F to 37 CFR part 1, subpart G, which will contain the updated
2009 version of the tables from WIPO Standard ST.25.
Section 1.821(c) is 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 the new Sec. 1.821(c)(1)-(3). Information
about sequence identifiers has been moved to Sec. 1.823(a).
Section 1.821(c)(1) is added to state 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.
1.823(b)(1),
[[Page 57042]]
is provided. Section 1.821(c)(2) is added to permit the submission of a
``Sequence Listing'' as a PDF file via the USPTO patent electronic
filing system. Section 1.821(c)(3) is added to permit the submission of
a ``Sequence Listing'' on physical sheets of paper.
Section 1.821(d) is 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'' will 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'' will be required to comply
with Sec. 1.821(e). 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 1.821(e)(1) is 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 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 ``Sequence
Listing,'' under Sec. 1.821(c), was submitted on physical sheets of
paper or as a PDF image file via the USPTO patent electronic filing
system.
Section 1.821(e)(2) is 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
(Sec. 1.821(c)(2)) or on physical sheets of paper (Sec. 1.821(c)(3)).
Section 1.821(e)(3) is 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) and where 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. 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 added to state that the CRF may not be
retained as a part of the patent application file.
Section 1.821(f) is reserved. The text previously found in this
section is now in Sec. Sec. 1.1821(e)(1)(ii) and 1.821(e)(2)(ii).
Section 1.821(g) is revised to delete the reference to Sec.
1.821(f). Additionally, Sec. 1.821(g) is 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 revised to reference paragraph (e)(3) of this
section instead of paragraphs (b) through (f). Section 1.821(h) is also
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 revised to remove all prior references to WIPO
Standard ST.25 (1998) and instead cross-reference new Appendices A
through F to 37 CFR part 1, subpart G, which 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 revised to remove the prior reference to
WIPO Standard ST.25 (1998) and instead cross-reference new Appendix A
to 37 CFR part 1, subpart G, which contains the updated 2009 version of
the standard.
Section 1.822(c)(3) is rewritten to replace instances of ``typed''
with ``listed.''
Section 1.822(c)(5) is rewritten to replace ``presented'' with
``represented.''
Section 1.822(c)(6) is rewritten to delete ``be marked'' and
instead state ``appear.''
Section 1.822(d)(1) is revised to remove the prior reference to
WIPO Standard ST.25 (1998) and instead cross-reference new Appendix C
to 37 CFR part 1, subpart G, which contains the updated 2009 version of
the standard.
Section 1.822(d)(3) is rewritten to replace ``presented'' with
``represented.''
Section 1.822(d)(4) is rewritten to replace ``presented'' with
``represented.''
Section 1.822(d)(5) is rewritten to replace the second occurrence
of ``presented'' with ``represented.''
Section 1.822(e) is rewritten to replace ``that is made up'' with
the term ``composed.''
Section 1.823
The title of Sec. 1.823 is rewritten as ``Requirements for content
of a `Sequence Listing' part of the specification.''
Section 1.823(a) is 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 revised to include a requirement for
applications, other than an international application
[[Page 57043]]
in the international stage, to contain, in the specification of the
patent application, an express incorporation by reference of the
material submitted as an ASCII plain text file via the USPTO patent
electronic filing system or on a read-only optical disc(s) identifying
the name of the file, the date of creation, and the size of the file in
bytes.
Section 1.823(b)(2) is revised to specifically exempt international
applications during the international stage from the incorporation by
reference requirement in Sec. 1.823(b)(1).
Section 1.823(b)(3) is 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 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 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)
sets forth the computer compatibilities and operating systems
permitted. Section 1.824(a)(2) indicates that ASCII plain text is
required, 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) sets forth the naming convention for the ASCII
plain text file of the ``Sequence Listing.'' Section 1.824(a)(4) is
revised 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) indicates 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) indicates 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 a read-only optical disc(s), in compliance with Sec.
1.52(e). Section 1.824(b)(2) provides that file compression may be
used, and it defines the parameters for file compression for submission
on a read-only optical disc. Section 1.824 is further revised to
eliminate obsolete media on which the CRF of a ``Sequence Listing'' may
be submitted. Section 1.824(c) is eliminated, since the types of media
available are specifically enumerated in Sec. 1.52(e). Section
1.824(d) is eliminated, since the same provision is now included in
Sec. 1.52(e)(6).
Section 1.825
Sections 1.825(a) and (b) are rewritten to distinguish between a
newly added ``Sequence Listing'' and an amended/replacement ``Sequence
Listing'' submission, respectively. Sections 1.825(a) and (b) are
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 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 updated to require an amended/replacement
``Sequence Listing'' be submitted (1) as an ASCII plain text file via
either the USPTO patent electronic filing system or on a read-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, the request can ask to incorporate by
reference the amended/replacement ``Sequence Listing,'' submitted as an
ASCII plain text file, in a separate paragraph of the specification
(replacing any prior such paragraph, as applicable) (Sec.
1.825(b)(2)). Second, the request can ask to insert, 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) replaces the current Sec. 1.825(c), which is
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, it must be amended to
contain such an incorporation by reference.
Section 1.825(d) contains the material from the current Sec.
1.825(c).
[[Page 57044]]
Subpart G of Part 1
Appendices A through F are added, explicitly incorporating the text
of Tables 1-6, Appendix 2, WIPO Standard ST.25 (2009) into the CFR.
Appendix G is added to incorporate the table that was previously
located in Sec. 1.823.
Comments and Responses
The USPTO published a proposed rule on May 26, 2021, at 86 FR
28301, soliciting public comment on the proposed amendments to 37 CFR
part 1 being adopted in this final rule. The USPTO received no comments
from the public on the proposed rule.
Rulemaking Considerations
A. Administrative Procedure Act
The changes 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 in this rulemaking were 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 chose to seek public comment before
implementing the rule to benefit from the public's input.
B. Regulatory Flexibility Act
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 amends 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 plain 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, is permitted if
compliant with certain new procedures. Other rules related to certain
obsolete and non-secure methods of presenting data are eliminated.
Lastly, this rule removes 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 ability 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 makes more flexible the process for submitting
large amounts of data and streamlines other procedural steps related to
data files associated with patent applications. This rulemaking's
changes are largely procedural in nature and do not impose any
additional requirements or fees on applicants. For the foregoing
reasons, the changes in this rule 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 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. 4, 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. 5, 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.), 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
[[Page 57045]]
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
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 rulemaking have been
submitted to OMB. Modifications include the removal of the Request for
Transfer of a Computer Readable Form Under 37 CFR 1.821(e) (Form PTO/
SB/93), which will result in a slight reduction in the 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 reduction estimates are
based on the prior OMB approved burdens (response volumes) associated
with this information collection, which may be different from any
forecasts mentioned in other parts of this rule.
The changes discussed in this rule do not affect the information
collection requirements or burdens associated with 0651-0031, 0651-
0032, and 0651-0064 listed above; therefore, the USPTO has not taken
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 amends 37 CFR part 1 as
follows:
PART 1--RULES OF PRACTICE IN PATENT CASES
0
1. The authority citation for 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 section 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 optical disc in compliance with
this paragraph (e):
(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]; and
(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
[[Page 57046]]
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 require 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 Sec. 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 in 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) Oversized submission. 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 points), but may be no smaller than 0.21cm (0.08 inches) high
(e.g., a font size of 6 points). 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 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; and
(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
[[Page 57047]]
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 disc copies 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 paragraph (g) of this section, 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
in 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 solving a problem,
regulating the flow of work in a computer, or controlling or monitoring
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 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
[[Page 57048]]
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 this paragraph (c), submitted via the USPTO patent
electronic filing system, or on a read-only optical disc, in compliance
with Sec. 1.52(e), where the replacement read-only optical disc must
be submitted in duplicate, and the read-only optical discs 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'';
(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
(Sec. 1.125), 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:
(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) and
(h) to read as follows:
[[Page 57049]]
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 to this subpart
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,'' which is 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:'' or the like, 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) of this
section 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
(paragraph (c)(2) of this section) or on physical sheets of paper
(paragraph (c)(3) of this section), and not also as an ASCII plain text
file, in compliance with Sec. 1.824 (paragraph (c)(1) of this
section), 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.
(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.
* * * * *
(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
[[Page 57050]]
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:
0
a. Revising paragraphs (b) and (c)(1), (3), (5) and (6);
0
b. Adding note 2 to paragraph (c);
0
c. Revising paragraphs (d)(1) and (3) through (5);
0
d. Adding note 3 to paragraph (d); and
0
e. Revising paragraph (e).
The revisions and additions 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 to this subpart
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 to this subpart
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 five 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 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 to this subpart
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 to
this subpart. 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
[[Page 57051]]
identifier enclosed in angle brackets, as shown in appendix G to this
subpart.
(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 a separate sequence identifier to each sequence,
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 to this subpart, 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]; and
(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; and
(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 a 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 Sec. 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) 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,
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'' 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:
[[Page 57052]]
(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 a certificate of
correction) must comply with the requirements of paragraph (b) of this
section.
0
15. Redesignate appendix A to subpart G of part 1 as appendix G to
subpart G, add appendices A through F to subpart G, and revise the
newly redesignated appendix G to read as follows:
Sec.
* * * * *
Appendix A to Subpart G of Part 1--List of Nucleotides
Appendix B to Subpart G of Part 1--List of Modified Nucleotides
Appendix C to Subpart G of Part 1--List of Amino Acids
Appendix D to Subpart G of Part 1--List of Modified and Unusual
Amino Acids
Appendix E to Subpart G of Part 1--List of Feature Keys Related to
Nucleotide Sequences
Appendix F to Subpart G of Part 1--List of Feature Keys Related to
Protein Sequences
Appendix G to Subpart G of Part 1--Numeric Identifiers
Appendix A to Subpart G of Part 1--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.
------------------------------------------------------------------------
Appendix B to Subpart G of Part 1--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.
[[Page 57053]]
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 to Subpart G of Part 1--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.
[[Page 57054]]
Tyr............................... Tyrosine.
Asx............................... Asp or Asn.
Glx............................... Glu or Gln.
Xaa............................... unknown or other.
------------------------------------------------------------------------
Appendix D to Subpart G of Part 1--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.
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 to Subpart G of Part 1--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.
[[Page 57055]]
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.
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).
[[Page 57056]]
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 to Subpart G of Part 1--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.
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, proline, or
HYDROXYLATION. 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.
[[Page 57057]]
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.
------------------------------------------------------------------------
Appendix G to Subpart G of Part 1--Numeric Identifiers
------------------------------------------------------------------------
Comments and Mandatory (M)
Numeric identifier Definition format or 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 ............... M.
Invention.
................ File Reference. Personal file M when filed
reference. prior to
assignment or
appl. number.
................ Current Specify as: US M, if
Application 09/999,999 or available.
Number. PCT/US09/99999.
................ Current Filing Specify as: M, if
Date. yyyy-mm-dd. available.
................ Prior Specify as: US M, if
Application 09/999,999 or applicable
Number. PCT/US09/99999. include
priority
documents
under 35
U.S.C. 119 and
120.
................ Prior Specify as: M, if
Application yyyy-mm-dd. applicable.
Filing Date.
................ Number of SEQ Count includes M.
ID NOs. total number
of SEQ ID NOs.
................ Software....... Name of O.
software used
to create the
``Sequence
Listing''.
................ SEQ ID NO:#:... Response shall M.
be an integer
representing
the SEQ ID NO
shown.
................ Length......... Respond with an M.
integer
expressing the
number of
bases or amino
acid residues.
................ Type........... Whether M.
presented
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 M.
name, i.e.,
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 M, under the
after . following
conditions: If
provide for a ``n,''
description of ``Xaa,'' or a
points of modified or
biological unusual L-
significance amino acid or
in the modified base
sequence. was used in a
sequence; if
ORGANISM is
``Artificial
Sequence'' or
``Unknown'';
if molecule is
combined DNA/
RNA.
[[Page 57058]]
................ Name/Key....... Provide M, under the
appropriate following
identifier for conditions: If
feature, from ``n,''
WIPO Standard ``Xaa,'' or a
ST.25 (2009), modified or
Appendices E unusual L-
and F to this amino acid or
subpart. modified base
was used in a
sequence.
................ Location....... Specify M, under the
location following
within conditions: If
sequence; ``n,''
where ``Xaa,'' or a
appropriate, modified or
state number unusual L-
of first and amino acid or
last bases/ modified base
amino acids in was used in a
feature. sequence.
................ Other Other relevant M, under the
Information. information; following
four lines conditions: If
maximum. ``n,''
``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 Leave blank O.
Information. after .
................ Authors........ Preferably max. O.
of 10 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 O.
which data
published;
specify as
yyyy-mm-dd,
MMM-yyyy or
Season-yyyy.
................ Database Accession O.
Accession number
Number. assigned by
database,
including
database name.
................ Database Entry Date of entry O.
Date. in database;
specify as
yyyy-mm-dd or
MMM-yyyy.
................ Patent Document Document O.
Number. number; for
patent-type
citations
only. Specify
as, for
example, US 09/
999,999.
................ Patent Filing Document filing O.
Date. date, for
patent-type
citations
only; specify
as yyyy-mm-dd.
................ Publication Document O.
Date. publication
date, for
patent-type
citations
only; specify
as yyyy-mm-dd.
................ Relevant FROM (position) O.
Residues. TO (position).
................ Sequence....... SEQ ID NO M.
should follow
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. 2021-22217 Filed 10-13-21; 8:45 am]
BILLING CODE 3510-16-P
