(157) DEPARTMENT OF COMMERCE
Patent and Trademark Office
37 CFR Part 1
[Docket No: 960828235-8109-02]
RIN: 0651-AA88
Requirements for Patent Applications
Containing Nucleotide Sequence and/or
Amino Acid Disclosures
AGENCY: Patent and Trademark Office, Commerce.
ACTION: Final Rule
SUMMARY: The Patent and Trademark Office (PTO) is amending the rules for
submitting nucleotide or amino acid sequences in computer readable form
(CRF) for patent applications.These amendments simplify the requirements
of the rules, rearrange portions of the rules for better understanding
and establish consistent rules to permit a single internationally
acceptable computer readable form. Sequence Listings will be presented
in an international, language neutral format using numeric identifiers
rather than the current subject headings. The Paper Sequence Listing
will preferably be a separately numbered section of the patent
application. Sequences which contain fewer than four specifically
identified nucleotides or amino acids will no longer be required to be
submitted in computer readable form.
DATES: EFFECTIVE DATE: July 1, 1998.
The incorporation by reference of certain publications listed in the
regulations is approved by the Director of the Federal Register as of
July 1, 1998.
APPLICABILITY DATE: Sections 1.821 through 1.825 as amended apply to
applications filed on or after July 1, 1998, except for: (1)
applications that claim the benefit of a prior application under 35
U.S.C. 120 filed before July 1, 1998, and which do not add subject
matter involving a sequence listing subject to 1.821 through 1.825;
and (2) reissue applications in which the application for the patent
sought to be reissued was filed before July 1, 1998. Sections 1.821
through 1.825 apply during a reexamination proceeding if the application
for the patent sought to be reexamined was filed on or after July 1,
1998.
FOR FURTHER INFORMATION CONTACT: Esther M. Kepplinger, by telephone at
(703) 308-1495; by mail addressed to: Box Comments - Patents, Assistant
Commissioner for Patents, Washington, DC 20231 marked to her attention;
by facsimile to (703) 305-3935; or by electronic mail at
esther.kepplinger@uspto.gov.
SUPPLEMENTAL INFORMATION: Sections 1.821 through 1.825 of title 37
provide a standardized format for the description of nucleotide and
amino acid sequence data in patent applications and require the
submission of such sequences in computer readable form (CRF).Sections
1.821 through 1.825 provide the following benefits to the PTO: (1)
improved search capabilities; (2) improved interference detection; (3)
more efficient examination; (4) cost savings for the input of the
sequence data; (5) more efficient and accurate printing of sequences in
patents; (6) exchange of the sequence data with other patent offices
electronically; and (7) improved public access to the sequences
electronically.
REASONS FOR THE CHANGES
In response to the needs of our customers, the procedural requirements
found in former 1.821 through 1.825 have been reduced. Sections
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1.821 through 1.825 are being amended to be consistent with World
Intellectual Property Organization (WIPO) Standard ST.25 (signed in 1998
and effective July 1, 1998). ST.25 replaces WIPO Standards ST.23 and
ST.24 which deal with paper and electronic submissions of sequence
listings.
A Meeting of International Authorities (MIA) under the Patent
Cooperation Treaty (PCT) was held in November of 1994 to discuss
simplification of sequence listing submission requirements.
Under the previous PCT Regulations, each International Searching
Authority, each International Preliminary Examining Authority and each
designated/elected office was free to set the requirements for
submission of sequence listings in paper and electronic form. This
imposed a burden on applicants by requiring them to prepare sequence
listings in many different formats. In addition, sequence listings were
required to be translated for consideration in the national stage at
considerable cost to applicants and at the risk that the information
could be inaccurately translated.
After the November 1994 MIA, the PTO, the European Patent Office (EPO)
and the Japanese Patent Office (JPO) worked together with WIPO to create
a new international standard which forms the basis of WIPO Standard
ST.25 (1998). Sections 1.821 through 1.825 of 37 CFR, as amended herein,
are consistent with WIPO Standard ST.25 (1998) and the PCT sequence
listing requirements. Sequence listings prepared in accordance with
1.821 through 1.825 as amended generally will be acceptable in all
countries which adhere to WIPO Standard ST.25 (1998). In addition, a
sequence listing prepared in accordance with the 1.821 through
1.825 as amended will be acceptable for the national stage in all PCT
member countries which require the submission of a sequence listing. As
a result of this rule change, applicants will experience a reduction in
cost since only one sequence listing in paper and electronic form will
need to be prepared and translations of this listing will not be needed.
All necessary changes to the text of 1.821 through 1.825 to reflect
the new WIPO Standard ST.25 (1998), have been made. Each change is
described below.
OVERVIEW OF THE CHANGES
The changes in this Final Rule include:
(1) use of numeric identifiers to replace the language subject
headings within the submission;
(2) elimination of unnecessary and confusing data elements;
(3) movement of the paper Sequence Listing to the end of the
application, preferably with separately numbered pages;
(4) elimination of the requirement to provide a submission for
sequences with fewer than four specifically defined nucleotides or amino
acids;
(5) use of lower-case one-letter codes for nucleotide bases;
(6) rearrangement of portions of the rules to improve their context;
(7) clarification and simplification of the rules to aid in
understanding; and
(8) minor changes to accomplish harmonization with WIPO Standard
ST.25 (1998) as well as the EPO and the JPO standards.
Amended 1.821 through 1.825 are not mandatory for: (1) applications
that claim the benefit of a prior application under 35 U.S.C. 120 filed
before July 1, 1998, and which do not add subject matter involving a
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sequence listing subject to 1.821 through 1.825; (2) reissue
applications in which the application for the patent sought to be
reissued was filed before July 1, 1998; and (3) reexamination
proceedings if the application for the patent sought to be reexamined
was filed before July 1, 1998. The PTO will accept and encourages the
submission of sequence listings in compliance with amended 1.821
through 1.825 for any application or reexamination proceeding. All
sequence listings (including the entire computer readable form) must be
submitted in compliance with either 1.821 through 1.825 as amended
in this Final Rule or (when permitted) former 1.821 through 1.825.
If the CRF for a new application would be identical to a compliant CRF
already on file in the PTO, the applicant may make reference to the
other application and the CRF in lieu of filing a duplicate CRF in the
new application by following the procedures set forth in 1.821(e). If
exceptional circumstances do arise and certain applicants experience
specific hardships in attempting to comply with amended 1.821
through 1.825, the PTO will consider a petition under 1.183 to waive
certain requirements of 1.821 through 1.825.
A Notice of Proposed Rulemaking entitled "Changes Implementing
Nucleotide and/or Amino Acid Sequence Listings" (Notice of Proposed
Rulemaking) was published in the Federal Register at 61 FR 51855
(October 4, 1996), and in the Official Gazette of the Patent and
Trademark Office, at 1191 Off. Gaz. Pat. Office 168 (October 29, 1996).
Sections 1.821 through 1.825 as adopted contain several changes from
these sections. This Final Rule provides a discussion of the content of
the specific rules being amended, description of the changes in the text
of the proposed rules, and explanation of the reasons supporting the
changes. In addition, comments received in response to the Notice of
Proposed Rulemaking are analyzed.
Discussion of Specific Rules and Changes from the Proposed Rules:
Title 37 of the Code of Federal Regulations, Part 1, is amended as
follows.
SECTION 1.77
The proposed change to 37 CFR 1.77 was previously adopted. See
Miscellaneous Changes to Patent Practice; Final Rule, 61 FR 42790
(August 19, 1996), 1190 Off. Gaz. Pat. Office 67 (September 17, 1996).
Section 1.821
Section 1.821 incorporates by reference the World Intellectual Property
Organization (WIPO) Handbook on Industrial Property Information and
Documentation, Standard ST.25 (1998), including Tables 1 through 6 of
Appendix 2, in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies
may be obtained from the World Intellectual Property Organization; 34
chemin des Colombettes; 1211 Geneva 20 Switzerland. Copies may be
inspected at the Patent Search Room; Crystal Plaza 3, Lobby Level; 2021
South Clark Place; Arlington, VA 22202. Copies may also be inspected at
the Office of the Federal Register, 800 North Capitol Street, NW, Suite
700, Washington, DC 20408. These Tables are reproduced below.
WIPO Standard ST.25 (1998), Appendix 2, Table 1, provides that the bases
of a nucleotide sequence should be represented using the following
one-letter code for nucleotide sequence characters:
Table 1: one letter codes for nucleotide sequences
Symbol Meaning Origin of
designation
a a adenine
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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 3
H-bonds
w a or t/u weak interactions 2
H-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 any
or t/u) or
(unknown
or other)
WIPO Standard ST.25 (1998), Appendix 2, Table 2, provides that modified
bases may be represented as the corresponding unmodified bases in the
sequence itself, if the modified base is one of those listed below and
the modification is further described in the Feature section of the
Sequence Listing. The codes from the list below may be used in the
description ( i.e., the specification and drawings, or in the Sequence
Listing) but these codes may not be used in the sequence itself.
Table 2: modified bases
Symbol Meaning
ac4c 4-acetyl cytidine
chm5u 5-(carboxyhydroxylmethyl)uridine
cm 2-O-methylcytidine
cmnm5s2u 5-carboxymethylaminomethyl-2-
thiouridine
cmnm5u 5-carboxymethylaminomethyluridine
d dihydrouridine
fm 2-O-methylpseudouridine
gal q beta, D-galactosylqueuosine
gm 2-O-methylguanosine
I inosine
i6a N6-isopentenyladenosine
m1a 1-methyladenosine
m1f 1-methylpseudouridine
m1g 1-methylguanosine
m1i 1-methylinosine
m22g 2,2-dimethylguanosine
m2a 2-methyladenosine
m2g 2-methylguanosine
m3c 3-methylcytidine
m5c 5-methylcytidine
m6a N6-methyladenosine
m7g 7-methylguanosine
mam5u 5-methylaminomethyluridine
mam5s2u 5-methoxyaminomethyl-2-thiouridine
man q beta, D-mannosylqueuosine
mcm5s2u 5-methoxycarbonylmethyl-2-thiouridine
mcm5u 5-methoxycarbonylmethyluridine
mo5u 5-methoxyuridine
ms2i6a 2-methylthio-N6-isopentenyladenosine
ms2t6a N-((9-beta-D-ribofuranosyl-2-
methylthiopurine-6-yl) carbamoyl)
threonine
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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
WIPO Standard ST.25 (1998), Appendix 2, Table 3, provides that the amino
acids should be represented using the following three-letter code with
the first letter as a capital.
Table 3: amino acid three-letter codes
Symbol Meaning
Ala Alanine
Cys Cysteine
Asp Aspartic Acid
Glu Glutamic Acid
Phe Phenylalanine
Gly Glycine
His Histidine
Ile Isoleucine
Lys Lysine
Leu Leucine
Met Methionine
Asn Asparagine
Pro Proline
Gln Glutamine
Arg Arginine
Ser Serine
Thr Threonine
Val Valine
Trp Tryptophan
Tyr Tyrosine
Asx Asp or Asn
Glx Glu or Gln
Xaa unknown or other
WIPO Standard ST.25 (1998), Appendix 2, Table 4, provides that modified
and unusual amino acids may be represented as the corresponding
unmodified amino acids in the sequence itself if the modified or unusual
amino acid is one of those listed below and the modification is further
described in the Feature section of the Sequence Listing. The codes from
the list below may be used in the description (i.e., the specification
and drawings, or in Sequence Listing) but these codes may not be used in
the sequence itself.
Table 4: modified and unusual amino acid codes
Symbol Meaning
Aad 2-Aminoadipic acid
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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-Diaminobu tyric 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
WIPO Standard ST.25 (1998), Appendix 2, Table 5 provides for feature
keys related to DNA sequences.
Table 5: Feature keys related to nucleotide sequences
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 up-stream of the start point of eukaryotic transcrip-
tion 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
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DNA, displacing the original partner DNA strand in this
region; also used to describe the displacement of a region
of one strand of duplex DNA by a single stranded invader in
the reaction catalyzed by RecA protein
D-segment diversity segment of immunoglobulin heavy chain, and
T-cell receptor beta chain
enhancer a cis-acting sequence that increases the utilization of
(some) eukaryotic promoters, and can function in either
orientation and in any location (upstream or downstream)
relative to the promoter
exon region of genome that codes for portion of spliced mRNA; may
contain 5'UTR, all CDSs, and 3'UTR
GC_signal GC box; a conserved GC-rich region located upstream of
the start point of eukaryotic transcription units which may
occur in multiple copies or in either orientation;
consensus=GGGCGG
gene region of biological interest identified as a gene and for
which a name has been assigned
iDNA Intervening DNA; DNA which is eliminated through any of
several kinds of recombination
intron a segment of DNA that is transcribed, but removed from
within the transcript by splicing together the sequences
(exons) on either side of it
J_segment joining segment of immunoglobulin light and heavy
chains, and T-cell receptor alpha, beta, and gamma-chains
LTR long terminal repeat, a sequence directly repeated at both
ends of a defined sequence, of the sort typically found in
retroviruses
mat_peptide mature peptide or protein coding sequence; coding
sequence for the mature or final peptide or protein product
following post-translational modification. The location does
not include the stop codon (unlike the corresponding CDS)
misc_binding site in nucleic acid which covalently or non-covalently binds
another moiety that cannot be described by any other Binding
key (primer_bind or protein_bind)
misc_dif- feature sequence is different from that presented in the
ference entry and cannot be described by any other Difference key
(conflict, unsure, old sequence, mutation, variation, allele,
or modified_base)
misc_eature 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_pep-
tide, mat_peptide, intron, polyA_site, rRNA, tRNA, scRNA, and
snRNA)
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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_struc- any secondary or tertiary structure or conformation that
ture cannot be described by other Structure keys (stem_loop
and D-loop)
modified_ the indicated nucleotide is a modified nucleotide and should
base 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_se- the presented sequence revises a previous version of
quence the sequence at this location
polyA_sig- recognition region necessary for endonuclease
nal cleavage of an RNA transcript that is followed by polyaden-
ylation; consensus=AATAAA
polyA_site site on an RNA transcript to which will be added adenine
residues by post- transcriptional polyadenylation
precur- any RNA species that is not yet the mature RNA product; may
sor_RNA 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_trans- primary (initial, unprocessed) transcript; includes 5'clipped
cript 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 replica-
tion, transcription, or reverse transcription. Includes
site(s) for synthetic e.g., PCR primer elements
promoter region on a DNA molecule involved in RNA polymerase binding
to initiate transcription
pro- non-covalent protein binding site on nucleic acid
tein_bind
RBS ribosome binding site
repeat_re- region of genome containing repeating units
gion
repeat_unit single repeat element
rep_origin origin of replication; starting site for duplication of
nucleic acid to give two identical copies
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rRNA mature ribosomal RNA; the RNA component of the ribonucleo-
protein 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) nucle-
us of a eukaryote
sig_peptide signal peptide coding sequence; coding sequence for an N-
terminal domain of a secreted protein; this domain is invol-
ved 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 permissi-
ble
stem_loop hairpin; a double-helical region formed by base-pairing
between adjacent (inverted) complementary sequences in a
single strand of RNA or DNA
STS Sequence Tagged Site. Short, single-copy DNA sequence that
characterizes a mapping landmark on the genome and can be
detected by PCR. A region of the genome can be mapped by
determining the order of a series of STSs
TATA_signal TATA box; Goldberg-Hogness box; a conserved AT-rich septamer
found about 25 bp before the start point of each eukaryotic
RNA polymerase II transcript unit which may be involved in
positioning the enzyme for correct initiation;
consensus=TATA(A or T)A(A or T)
terminator sequence of DNA located either at the end of the transcript
or adjacent to a promoter region that causes RNA polymerase
to terminate transcription; may also be site of binding of
repressor protein
trans- transit peptide coding sequence; coding sequence for an
it_peptide 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
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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
(e.g., 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 [ ]
WIPO Standard ST.25 (1998), Appendix 2, Table 6 provide for feature keys
related to protein sequences.
Table 6: Feature keys related to Protein sequences
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-CARBOXYGLU- Of asparagine, aspartic acid, proline or lysine
TAMIC ACID HYDROXY-
LATION
METHYLATION Generally of lysine or arginine
PHOSPHORYLATION Of serine, threonine, tyrosine, aspartic acid or
histidine
PYRROLIDONE CAR- N-terminal glutamate which has formed an internal
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BOXYLIC ACID 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 throughan 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 rep-
resent the two residues which are linked by an
intra-chain disulfide bond. If the `FROM' and `TO'
endpoints are identical, the disulfide bond is an
interchain one and the description field indicates
the nature of the cross-link
THIOLEST Thiolester bond. The `FROM' and `TO' endpoints
represent the two residues which are linked by the
thiolester bond
THIOETH Thioether bond. The `FROM' and `TO' endpoints
represent the two residues which are linked by the
thioether bond
CARBOHYD Glycosylation site. The nature of the carbohydrate
(if known) is given in the description field
METAL Binding site for a metal ion. The description field
indicates the nature of the metal
BINDING Binding site for any chemical group (co-enzyme,
prosthetic group, etc.). The chemical nature of the
group is given in the description field
SIGNAL Extent of a signal sequence (prepeptide)
TRANSIT Extent of a transit peptide (mitochondrial,
chloroplastic, or for a microbody)
PROPEP Extent of a propeptide
CHAIN Extent of a polypeptide chain in the mature protein
PEPTIDE Extent of a released active peptide
DOMAIN Extent of a domain of interest on the sequence.
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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, e.g., Alpha-helix,
3(10) helix, or Pi-helix
STRAND Secondary structure - Beta-strand, e.g., Hydrogen
bonded beta-strand, or Residue in an isolated
beta-bridge
TURN Secondary structure - Turns, e.g., 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
In paragraph (a) of 1.821, the reference to "Standard ST.23:
Recommendation for the presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications and in Published Patent
Documents, paragraphs 8 through 12, April 1994" has been replaced by
"Standard ST.25: Standard for the Presentation of Nucleotide and Amino
Acid Sequence Listings in Patent Applications (1998), including Tables 1
through 6 in Appendix 2." These changes reflect the correct information
with regard to the incorporated WIPO standard and the lists of symbols
for nucleotide and amino acid sequence characters.
Further in paragraph (a) of 1.821, "(Hereinafter "WIPO Standard ST.23
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(April, 1994)")" has been changed to "(Hereinafter "WIPO Standard ST.25
(1998))." This change is necessary to indicate the correct abbreviation
for new standard ST.25.
Further in paragraph (a) of 1.821, both occurrences of "Copies of
ST.23" have been changed to "Copies of WIPO Standard ST.25 (1998)." This
change is necessary to reflect the new standard number.
In paragraph (a)(1) of 1.821, "ST.23 (April 1994), paragraph 8" has
been changed to "ST.25 (1998), Appendix 2, Table 1." This change
reflects the correct information with regard to the incorporated WIPO
standard and the list of symbols to be used for nucleotide sequence
characters.
Further in paragraph (a)(1) of 1.821, "ST.23 (April 1994), paragraph
9" has been changed to "ST.25 (1998), Appendix 2, Table 2." This change
reflects the correct information with regard to the incorporated WIPO
standard and the list of modified bases which can be presented as
unmodified nucleotide sequence characters.
In paragraph (a)(2) of 1.821, all three occurrences of "ST.23 (April
1994), paragraph 11" have been changed to "ST.25 (1998), Appendix 2,
Table 3." This change reflects the correct information with regard to
the incorporated WIPO standard and the list of symbols to be used for
amino acid sequence characters.
Further in paragraph (a)(2) of 1.821, "ST.23 (April 1994), paragraph
12" has been changed to "ST.25 (1998), Appendix 2, Table 4." This change
reflects the correct information with regard to the incorporated WIPO
standard and the list of modified or unusual amino acids which can be
presented as unmodified amino acid sequence characters.
In paragraph (c) of 1.821, each of the three occurrences of the words
"integer identifier" or "integer identifiers" has been changed to
"sequence identifier" or "sequence identifiers" as appropriate. WIPO
Standard ST.25 (1998), uses the term "sequence identifier" rather than
"integer identifier." Thus, this change is necessary to achieve
harmonization with the international standard.
In the last sentence of paragraph (c) of 1.821, the phrase "The
sequence omitted shall appear following the integer identifier" of the
proposed rule has been replaced by the code `000' shall be used in place
of the sequence." The response for the numeric identifier <160> shall
include the total number of SEQ ID NOs, whether followed by a sequence
or by the code "000". The code <000> should be put into <400>. This
change permits flexibility in the preparation and amendment of Sequence
Listings. It also makes the rule language-neutral and is consistent with
WIPO Standard ST.25 (1998).
In paragraph (d) of 1.821, the words "integer identifier" have been
changed to "sequence identifier." WIPO Standard ST.25 (1998) uses the
term "sequence identifier" rather than "integer identifier." Thus, this
change is necessary to achieve harmonization with the international
standard.
In paragraphs (f), (g) and (h) of 1.821, the sentence "Such a
statement must be a verified statement if made by a person not
registered to practice before the Office" has been deleted. The separate
verification requirements in 1.821 have been eliminated in view of
the recent amendment to 1.4(d) and 10.18. See Changes to Patent
Practice and Procedure; Final Rule, 62 FR. 53131 (October 10, 1997),
1203 Off. Gaz. Pat. Office 63 (October 21, 1997). Paragraph (g) of
1.821 has also been amended to provide that the Office will provide a
"period of time" (rather than one month) within which the applicant must
comply with the requirements of 1.821(b) through (f) in order to
avoid abandonment.
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Further in paragraph (f) of 1.821, the following has been added at
the end of the first sentence, ", e.g., the information recorded in
computer readable form is identical to the written sequence listing."
WIPO Standard ST.25 (1998), paragraph 39, requires the language which
has been added as an acceptable example for phrasing the required
statement that the computer readable form and the written sequence
listing are the same.
Section 1.822
In paragraph (b) of 1.822, both references to WIPO Standard ST.23
(April 1994), paragraphs 8 and 11, as proposed have been changed to
"WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3." These changes
reflect the correct information with regard to the incorporated WIPO
standard and the lists of symbols for nucleotide and amino acid sequence
characters.
Further in paragraph (b) of 1.822, "WIPO Standard ST.23 (April
1994), paragraphs 9 and 12" as proposed has been changed to "WIPO
Standard ST.25 (1998), Appendix 2, Tables 2 and 4." This change reflects
the correct information with regard to the incorporated WIPO standard
and the lists of modified bases and modified or unusual amino acids
which can be depicted in the Sequence Listing via the symbols for a
corresponding unmodified base or amino acid.
Further in paragraph (b) of 1.822, the symbol designating an unknown
nucleotide base or a nucleotide base other than those listed in the WIPO
standard was proposed as an upper case letter "N." This symbol has been
changed to a lower case letter "n." This change is consistent with the
use of lower case letters for the symbols representing the nucleotide
bases. Further in paragraph (b) of 1.822, the language has been
clarified to specifically state that each "n" or "Xaa" represents only a
single residue. Thus, for example, a single "Xaa" may not be used to
designate a string of four amino acids, each of which is unknown. This
represents a codification of existing practice.
Further in paragraph (b) of 1.822, the information required in the
Feature section to explain the use of "n" or "Xaa" in a given sequence
is referred to "as appropriate." Additional instruction is added at the
end of paragraph (b) of 1.822 following "the Feature section"
indicating ", preferably by including one or more feature keys listed in
WIPO Standard ST.25 (1998), Appendix 2, Tables 5 and 6." This change
specifies the preference for using the feature keys listed in the WIPO
standard in order to aid applicants in filing a CRF which will comply
with WIPO Standard ST.25 (1998). These feature keys are controlled
vocabulary and are considered language neutral. Their use is required in
a PCT patent application or a patent application in a foreign country
which has adopted WIPO Standard ST.25 (1998).
In paragraph (c)(1) of 1.822, "WIPO Standard ST.23 (April 1994),
paragraph 8" as proposed has been changed to WIPO Standard ST.25 (1998),
Appendix 2, Table 1." This change reflects the correct information with
regard to the incorporated WIPO standard and the list of symbols to be
used for nucleotide sequence characters.
In paragraph (d)(1) of 1.822, "WIPO Standard ST.23 (April 1994),
paragraph 11, as proposed has been changed to "WIPO Standard ST.25
(1998), Appendix 2, Table 3." This change reflects the correct
information with regard to the incorporated WIPO standard and the list
of symbols to be used for amino acid sequence characters.
In paragraph (d)(4) of 1.822, the section notes that enumeration
requirements are applicable to amino acid sequences that are circular in
configuration. The following language has been added to the end of the
paragraph ", with the exception that the designation of the first amino
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acid of the sequence may be made at the option of the applicant." This
change is necessary to provide consistency with its counterpart of
circular nucleotide sequences as provided in paragraph (c)(7) of
1.822. This change is also consistent with WIPO Standard ST.25 (1998),
paragraph 21. In paragraph (e) of 1.822, the words "integer
identifiers" have been changed to "sequence identifiers." WIPO Standard
ST.25 (1998) uses the term "sequence identifier" rather than "integer
identifier." Thus, this change is necessary to achieve harmonization
with the international standard.
Section 1.823
In paragraph (a) of 1.823, the entire second sentence which read "On
a separate page of the application specification, immediately prior to
the claims, there shall be a reference to the presence of the `Sequence
Listing' in a `Sequence Listing Annex.'" has been eliminated. The
designation of the Sequence Listing as an annex to the specification was
initially proposed in an early version of the international standard.
This terminology is not used in WIPO Standard ST.25 (1998), however, and
so it has also been eliminated from paragraph (a) of 1.823, as
proposed. Simplification results as well by the elimination of the
requirement that the Sequence Listing must be designated as an annex to
the specification.
In paragraph (a) of 1.823, the third sentence has been modified by
deleting the words "shall appear in the `Sequence Listing Annex,' which
is." As explained above, the current version of the international
standard does not require designating the Sequence Listing as an annex
to the specification.
In paragraph (a) of 1.823, the words "preferably should be" have been
added to the third sentence, before "numbered independently of the
numbering of the remainder of the application" to describe the
independent page numbering of the Sequence Listing in paper copy form.
The term "preferably" was added for purposes of harmonization with WIPO
Standard ST.25 (1998). In paragraph (a) of 1.823, the last clause of
the third sentence "and shall be placed in the application file" has
been deleted as unnecessary and potentially confusing now that the
reference to a "Sequence Listing Annex" has been removed from this
paragraph. In paragraph (a) of 1.823, the fourth sentence has been
eliminated in its entirety. As explained above, the current version of
the international standard does not require designating the Sequence
Listing as an annex to the specification.
In paragraph (a) of 1.823, in both occurrences in the fifth sentence
and in the single occurrence in the sixth sentence, the word "shall" has
been changed to "should." These changes are necessary for purposes of
achieving consistency with WIPO Standard ST.25 (1998). In paragraph (b)
of 1.823, the first sentence has been modified by the deletion of the
words "in addition to and immediately preceding." This change is
consistent with WIPO Standard ST.25 (1998).
In paragraph (b) of 1.823, the fifth sentence has been deleted,
eliminating the prohibition of any item of information occupying more
than one line. This change is consistent with WIPO Standard ST.25 (1998).
In paragraph (b) of 1.823, the last sentence has been deleted to
eliminate the "rep" designation for data elements of the "Sequence
Listing." Certain data elements may still be repeated within the listing
but this change was made for harmonization of the table with WIPO
Standard ST.25 (1998).
In paragraph (b) of 1.823, the eighth sentence has been modified to
reflect the new numeric numbering scheme, for harmonization with WIPO
Standard ST.25 (1998). Specifically, "<100> through <193>" of the
proposed rule has been changed to "<110> through <170>." The table in
paragraph (b) of 1.823, has been changed to reflect the revised
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numbering scheme and data elements used in WIPO Standard ST.25 (1998).
The specific changes are as follows:
Numeric identifier "<100>, General Information," has been deleted from
the proposed rules, as it is not present in WIPO Standard ST.25 (1998).
Numeric identifier "<110>, Applicant," in the proposed rule, has been
changed to indicate that"preferably " a maximum of ten names may be
indicated. This change allows for more than ten names in the Applicant
field for those instances in which such would be appropriate. This
change is consistent with WIPO Standard ST.25 (1998).
Numeric identifier "<120>, Title of Invention," in the proposed rule,
has been changed to eliminate the limitation that the title be a maximum
of four lines. This change allows applicants more flexibility with
respect to the title. This change is consistent with WIPO Standard ST.25
(1998).
Numeric identifier "<130>, Number of Sequences," in the proposed rule,
has been changed to reflect "<130>, File Reference," as stated in WIPO
Standard ST.25 (1998). This numeric identifier was indicated as "<183>,
File Reference/Docket Number", in the rule as proposed.As proposed this
was an optional numeric identifier. The numeric identifier remains
optional once the application has been assigned an application number,
e.g., a serial number. This numeric identifier is now MANDATORY when an
application number has not yet been assigned to the application, such as
on the day the application is initially filed. This change will assist
in the matching of sequence information submissions with an application
in the event that either the paper copy or the computer readable form
were to become separated from the remainder of the application. This
change is consistent with WIPO Standard ST.25 (1998).
The Number of Sequences field identified as "<130>" in the proposed
rule is now numbered"<160>" in 1.823 as adopted and redefined as
"Number of SEQ ID NOs." The information associated with numeric
identifiers "<140>" through "<153>,""Correspondence Address " through "
Operating System " of the proposed rule, has been eliminated to reduce
the burden on the applicant and to harmonize with WIPO Standard ST.25
(1998). Some of these numeric identifiers have been used in the new
numbering scheme and have been associated with different information as
indicated herein and in the Table of 1.823.One remaining numeric
identifier within the Computer Readable Form section, "<154>, Software,"
of the proposed rule, will remain, with the exception that it has been
reassigned the numeric identifier of "<170>" to reflect the numbering
scheme presented in WIPO Standard ST.25 (1998).
The main headings "<160>, Current Application Data " and "<170>, Prior
Application Data," of the proposed rules, have been eliminated to
harmonize with WIPO Standard ST.25 (1998) and reduce the number of
fields in the Sequence Listing. The information that was to appear under
these main headings remains in the rules but has been reassigned numeric
identifiers<140> through<151>. The specific changes are as follows:
"<160>" has been redefined as "Number of SEQ ID NOs "; "<161>,
Application Number," of the proposed rule is now numbered as"<140>," and
is defined as "Current Application Number"; "<162>, Filing Date," of the
proposed rule is now numbered "<141>," and is defined as "Current Filing
Date"; "<170>" has been redefined as "Software "; "<171>, Application
Number," of the proposed rule is now numbered as "<150>," and is defined
as "Prior Application Number"; "<172>, Filing Date," of the proposed
rule is now numbered as "<151>," and is defined as "Prior Application
Filing Date."
The numeric identifiers now numbered "<150>, Prior Application Number,",
and "<151>, Prior Application Filing Date," are now mandatory only in
those instances in which a claim for priority with respect to those
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prior applications is being made under either 35 U.S.C. 119 or 120.This
change will provide information in this regard when it is most useful
and was necessary to harmonize these rules with WIPO Standard ST.25
(1998). Throughout the Sequence Listing, application numbers must be set
forth as a combination of the two digit country code, as set forth in
WIPO Standard ST.3, as well as an application number in accordance with
WIPO Standard ST.13 or for an international application, the numbering
system as set out in Section 307(a) of the Administrative Instructions
under the PCT.
Numeric identifiers "<180>, Attorney/Agent Information," through "<182>,
Registration Number," of the proposed rule, have been eliminated to
harmonize with WIPO Standard ST.25 (1998) and reduce the number of
fields in the Sequence Listing.
Numeric identifier "<183>, File Reference/Docket Number " of the
proposed rule has been reassigned as numeric identifier "<130>," and
redefined as "File Reference" in an effort to harmonize with WIPO
Standard ST.25 (1998).
The Telecommunication Information section, "<190>" through "<193>" of
the proposed rules, has been eliminated in order to reduce the number of
fields in the Sequence Listing and harmonize with WIPO Standard ST.25
(1998).
Numeric identifier "<200>, Information for SEQ ID NO:#:", has been
reassigned the numeric identifier "<210>, SEQ ID NO: #:" This numeric
identifier indicates the integer, referred to in these final rules as
the sequence identifier for both the sequence information and the actual
sequence which follows the information.
Numeric identifier "<210>, Sequence Characteristics," of the proposed
rule has been eliminated in order to reduce the number of required
elements in the Sequence Listing and harmonize with WIPO Standard ST.25
(1998).
The valid responses for the mandatory numeric identifier "<212>, Type,"
have been changed from "N" and "A", as stated in the proposed rule, to
"DNA," "RNA," and "PRT" (protein) in order to harmonize with WIPO
Standard ST.25 (1998). A compound that is a mixture of DNA and RNA
should be represented by "DNA." This change is consistent with WIPO
Standard ST.25 (1998).
Numeric identifier "<213>, Organism," has been added to the Sequence
Listing of these final rules in an effort to harmonize with WIPO
Standard ST.25 (1998). A response for the Organism identifier is
MANDATORY. The valid responses are the scientific name, i.e. "Genus
species", "Artificial Sequence", or "Unknown."
Numeric identifier "<214>, Topology," of the proposed rule, has been
eliminated to harmonize with WIPO Standard ST.25 (1998), and to reduce
the burden on the applicant.
Numeric identifier "<290>, Feature," has become numeric identifier
"<220>, Feature." This numeric identifier has become MANDATORY for those
sequences in which numeric identifier "<213>, Organism," is completed
with either "Artificial Sequence" or "Unknown." This numeric identifier
is also required if the compound sequence is a mixture of DNA and RNA.
Numeric identifier "<220>, Feature" is a header only. No data are added
immediately following this numeric identifier. These changes are
required to achieve harmonization with WIPO Standard ST.25 (1998).
Numeric identifier "<291>, Name/Key," has become numeric identifier
"<221>, Name/Key."As proposed, the information provided was restricted
to a maximum of four lines. The four line restriction has been removed
to reduce the limitations on this field. The comment section of this
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numeric identifier has been changed in that it now indicates that the
selection of a feature name or feature key is preferably made from those
listed in Tables 5 and 6 of WIPO Standard ST.25 (1998). These tables are
reproduced above and this preference for the listed feature names and
keys is consistent with the requirement of WIPO Standard ST.25 (1998).
Numeric identifier "<292>, Location," has become "<222>, Location," so
as to be consistent with the numeric identifiers contained in WIPO
Standard ST.25 (1998).
Numeric identifier "<294>, Other Information," has become numeric
identifier "<223>, Other Information," so as to be consistent with the
numeric identifiers contained in WIPO Standard ST.25 (1998). This
numeric identifier has become MANDATORY for those sequences in which
numeric identifier "<213>, Organism," is completed with either
"Artificial Sequence" or "Unknown". Numeric identifier "<223>, Other
Information," should contain source information in those instances when
the organism is unknown or is an artificial sequence. For example, the
source may be unknown because the material was isolated from a mixed
bacterial culture rather than a pure culture. In such a case, numeric
identifier "<223>, Other Information," should be completed by
explaining the mixed culture source of the sequenced material. If a
sequence is completely synthesized this should be indicated in numeric
identifier "<223>, Other Information," while numeric identifier "<213>,
Organism," would indicate "Artificial Sequence." This change has been
made to accomplish harmonization between these rules and WIPO Standard
ST.25 (1998) which contains the same mandatory requirement in this
regard. Numeric identifiers "<308>" through "<310>," referring to the "
Patent Document Number," "Filing Date " and " Publication Date," of the
proposed rule, have been moved to numeric identifiers "<310>" to
"<312>," respectively, of this Final Rule in order to harmonize with the
numeric numbering scheme of WIPO Standard ST.25 (1998). Citations in the
Sequence Listing must comply with WIPO Standard ST.6 for publication
numbers and WIPO Standard ST.16 for document codes.
New numeric identifiers "<308>, Database Accession Number," and
"<309>Database Entry Date," have been added to the final rules to
harmonize with WIPO Standard ST.25 (1998).These fields were added to the
publication information section of WIPO Standard ST.25 (1998) to give an
applicant more opportunity to further identify a published citation.
Numeric identifier<400> " Sequence Description: SEQ ID NO: #: has
been changed to "Sequence " for clarity. Also for clarity, the
explanation in the table has been changed to "SEQ ID NO shall follow the
numeric identifier and should appear on the line preceding the
sequence." The format of the date fields has been changed throughout the
Sequence Listing to accommodate for international conventions. All date
fields referenced in the Sequence Listing shall conform to WIPO Standard
ST.2. Because compliance with 1.821 through 1.825 as amended should
produce Sequence Listings that are acceptable to all receiving offices,
a standardized date field convention was required.
Section 1.824
In paragraph (a)(6) of 1.824, ", the date on which the data were
recorded on the computer readable form" was added after "title of the
invention" to harmonize with WIPO Standard ST.25 (1998) requirements.
While this requirement of 1.824 was proposed to be eliminated, that
proposal is not adopted for purposes of harmonization with WIPO Standard
ST.25 (1998). Also in paragraph (a)(6) of 1.824, " name and type of
computer and" was deleted to reduce the requirements.
Section 1.825
In paragraphs (a), (b), and (d) of 1.825, the sentence "Such a
statement must be a verified statement if made by a person not
registered to practice before the Office" has been deleted. The separate
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verification requirements in 1.825 have been eliminated in view of
the recent amendment to 1.4(d) and 10.18. See Changes to Patent
Practice and Procedure; Final Rule, 62 FR. 53131 (October 10, 1997),
1203 Off. Gaz. Pat. Office 63 (October 21, 1997).
Response to and Analysis of Comments
Six written comments were received in response to the Notice of Proposed
Rulemaking. Several of these comments address the three specific queries
set forth in the Notice of Proposed Rulemaking.
The first query posed in the Notice of Proposed Rulemaking was: (1)
Should the PTO accept voluntary submissions of computer readable forms
and Sequence Listings where a D-amino acid is contained in the sequence?
If such voluntary submissions are accepted, should there be a
restriction on the choice of identifying a D-amino acid by an Xaa or by
its L-amino acid counterpart abbreviation?
Comment: One comment indicated that not only should the PTO accept
voluntary submissions under these rules where a D-amino acid is
contained in the sequence, the Office should make such submissions
mandatory and designated by an Xaa. One comment indicated that sequences
containing D-amino acids should not be in the PTO databases.
Response: Upon careful consideration, the PTO has decided to accept
voluntary submissions of protein sequences containing D-amino acids. The
PTO strongly encourages anyone making such voluntary submissions to
identify a D-amino acid with an Xaa, describing the D-amino acid in the
Features section of the Sequence Listing. This section is indicated by
numeric identifiers<220>through<223> in 37 CFR 1.823. Procedural
concerns compel this acceptance of voluntary submissions. Computer
readable forms are processed prior to examination. It is cumbersome to
establish a viable procedure to redact any voluntary submissions out of
the PTO database. The use of Xaa to indicate a D-amino acid, should such
sequence information be submitted in accordance with these rules, is
encouraged so as to alert anyone reviewing the sequence that a
particular amino acid is other than a naturally occurring L-amino acid
and to more accurately depict the extent of similarities between such a
sequence and the L-amino acid containing sequences present in a database
being searched for examination or other purposes.
Because the sequence databases do not currently include D-amino acids in
sequences and thus are not searchable for such sequences, the submission
of those sequences containing D-amino acids will not be made mandatory.
The second query posed in the proposed rules was: (2) Should the
provisions of 37 CFR 1.821(c) be altered to exclude some prior art
sequences from inclusion in the Sequence Listing even though they are
presented in a patent application disclosure as sequences? Should the
reference to an accession number of an admitted prior art sequence in a
publicly available, electronic, sequence database suffice and exclude
that sequence from the requirements of the sequence rules?
Comment: Four comments indicated that known "prior art" sequences should
not be required in the Sequence Listing. A referral to a publicly
available, electronic, sequence database for access to such "prior art"
sequences would be an acceptable alternative to two of those commenting
on this aspect; the other two did not address this point. The reasons
given for excluding such sequences are the expense and time required by
applicants and their representatives in the inclusion of "prior art"
sequences that are considered to be "non-inventive". Reducing the bulk
of the paper copy of the Sequence Listing was also mentioned.
Response: The requirement to submit all disclosed sequences in the
format required by 1.821 through 1.825 is maintained. This point
was discussed with officials from the JPO and EPO.The offices have
considered the stated concerns with regard to costs to applicants.
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Sections 1.821 through 1.825 do not require any information to be
disclosed in the form of a sequence, but rather require a particular
format whenever information is presented in the form of a sequence.Those
applicants for whom compliance with the rules remains a significant
hardship may petition under 1.183 for a waiver of the applicable
requirement of 1.821 through 1.825.
The technical and legal concerns mentioned in the Notice of Proposed
Rulemaking still exist concerning the use of an alternative reference to
a publicly available, electronic, sequence database. These concerns are:
(1) What constitutes a publicly available, electronic, sequence
database? (2) Would the USPTO and the other patent offices which have
similar rules be required to produce a list of internationally accepted
databases? (3) What would be the criteria for such acceptance? (4) An
additional issue would exist involving electronic records maintenance:
is there any assurance that once information is contained in a database
that it will be retained and available indefinitely without alteration?
Changes to the information in nucleic acid sequence databases resulting
from the discovery of sequencing errors are well-known. (5) Does the
mere existence of the sequence information in such a record constitute
reasonable means of retrieval? In other words, would one need some text
basis or other identifier to retrieve the information?
Additional reasons for the inclusion of these prior art sequences remain
relevant. These reasons are: (1) the assessment of whether a particular
sequence falls within the requirements of the current rules is simple;
(2) the general public is assured that all patents which contain any
sequence information contain all of the sequence information in the
Sequence Listing and all sequences are available in a computer
accessible form; and (3) as a publication, the contextual association of
new and old information is potentially unique to the patent and very
valuable to anyone assessing the state of the art at the time of a
patented invention, and thus are desirable to be present in electronic
form in association with that patent.
The third query posed in the proposed rules was: (3) Should Sequence
Listings filed in an international application filed under the PCT be
published only electronically and made available for retrieval
electronically by an accession number from several sequence repositories?
Comment: Two comments were received in response to this query, one in
favor and one opposed to limiting the publication of the Sequence
Listing to an electronic form for published PCT applications in the
international phase.
Response: At this time paper copies of the Sequence Listings filed as
part of the description will continue to be published in applications
filed under PCT. The PTO together with the EPO, JPO and WIPO will
continue to discuss the possibility of electronic publication. However,
any implementation of such electronic publication in lieu of publication
in paper form will not be undertaken until further study has been
completed.
Comment: One comment suggested that informative English words be placed
next to the numerical headings in the Sequence Listing as printed in a
U.S. patent.
Response: The PTO will provide English words corresponding to the
numeric identifiers in the printed U.S. patents.
Comment: One comment suggested addition of a descriptive comment line to
the Sequence Listing.
Response: The "Other Information" line in the Features section, which is
numeric identifier <223> in 1.823, provides for a description of a
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sequence. While completion of this section is only mandatory when the
sequence contains "n", "Xaa", a modified or unusual L-amino acid or a
modified base, it is frequently completed in other circumstances.
Comment: One comment requested we harmonize 1.821 through 1.825
with PCT, EPO and other authorities such that the differences in the
requirements for Sequence Listing submissions are minimal.
Response: This change to 1.821 through 1.825 is the result of such
an effort to harmonize the PTO, PCT, EPO and JPO Sequence Listing
requirements to the extent possible. The requirements of newly developed
WIPO ST.25 are substantially identical to the requirements of amended
1.821 through 1.825. PatentIn Version 2.0 software, now available, is
drafted to meet all of the requirements of WIPO Standard ST.25 (1998).
The requirements of 1.821 through 1.825, however, are less
stringent than the requirements of WIPO Standard ST.25 (1998). Thus,
applicants who wish to file in countries which adhere to WIPO Standard
ST.25 (1998) should consider the following when not using PatentIn
Version 2.0:
1. The WIPO Standard ST.25 (1998) does not permit submissions using a
Macintosh computer.
2. The WIPO Standard ST.25 (1998) does not accept the range of media
permitted by amended 1.821 through 1.825.
3. The answers in field <221> and <222> must use selections from Tables
5 and 6 of WIPO Standard ST.25 (1998) to comply with that standard. The
terms from these Tables are considered language neutral vocabulary.
4. Any free text in numeric identifier <223> of a Sequence Listing will
not be translated and thus must also appear in the specification of
applications filed under WIPO Standard ST.25 (1998) for compliance.
5. A CRF filed after the filing of an application under the PCT does not
form part of the disclosure and will not be published in the pamphlet.
6. Paragraph 39 of WIPO Standard ST.25 (1998) requires the specific
wording "the information recorded on the form is identical to the
written sequence listing."
7. WIPO Standard ST.25 (1998), paragraph 24, requires spaces between
specified numeric identifiers in the Sequence Listing.
Comment: One comment requested a WINDOWS based version of PatentIn.
Response: A WINDOWS based version of PatentIn, PatentIn 2.0, has been
developed through a Trilaterally-sponsored joint initiative and is being
made available.
Comment: One comment expressed concern over application of the doctrine
of equivalents by the courts to sequence-based claim language.
Response: Sections 1.821 through 1.825 do not establish a disclosure
requirement, nor do they alter the requirements of 35 U.S.C. 112.
They merely require a particular format whenever information is
presented in the form of a sequence. The use of sequence identification
numbers (SEQ ID NO: #) only provides a shorthand way for applicants to
refer to sequence information.These identification numbers do not in any
way restrict the manner in which an invention can be claimed. Similarly,
the use of this format does not impact the potential interpretations and
legal determinations that could be made with respect to claims
containing information in the form of a nucleotide or amino acid
sequence.
Comment: One comment requested the flexibility to use single-letter
amino acid codes.
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Response: Sections 1.821 through 1.825 as amended do not constrain an
applicant from using single letter codes in the disclosure. The
requirements of the sequence searching and the sequence storage
mechanisms include only the three-letter codes, thus the need for the
constraint on the Sequence Listing information. There is no such
restriction on the sequence format in the body of the disclosure or in
the figures imposed by 1.821 through 1.825, or any of the rules of
practice; only the format for the Sequence Listing is specified by
1.821 through 1.825.
Review Under the Paperwork Reduction Act of 1995.
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 (PRA) unless that collection of information
displays a currently valid OMB control number.
This rule contains collections of information requirements subject to
the PRA. The principal impact of this Final Rule is: (1) elimination of
certain requirements of 1.821 through 1.825; and (2) revision of
1.821 through 1.825 for consistency with WIPO Standard ST.25 (1998),
which will permit Sequence Listings to be presented in an international,
language neutral format. The public reporting burden for these
collections of information have been approved by the Office of
Management and Budget (OMB) under OMB control number 0651-0024. The
public reporting burden for this collection of information is estimated
to average 80 minutes per response, including the time for reviewing
instructions, searching existing data sources, gathering and maintaining
the information. Send comments regarding this burden estimate or any
other aspect of the data requirements, including suggestions for
reducing this burden, to Esther M. Kepplinger at the address specified
above or to the Office of Information and Regulatory Affairs of OMB, New
Executive Office Bldg., 725 17th St. NW, rm. 10235, Washington, DC
20230, Attn: Desk Officer for the Patent and Trademark Office.
Other Considerations.
This Final Rule is in conformity with the requirements of the Regulatory
Flexibility Act (5 U.S.C. 601 et seq.), Executive Order 12612 (October
26, 1987), and the Paperwork Reduction Act of 1995 (44 U.S.C. 3501 et
seq.). It has been determined that this rulemaking is not significant
for the purposes of Executive Order 12866 (September 30, 1993).
The Assistant General Counsel for Legislation and Regulation of the
Department of Commerce has certified to the Chief Counsel for Advocacy,
Small Business Administration that this Final Rule would not have a
significant impact on a substantial number of small entities (Regulatory
Flexibility Act, 5 U.S.C. 605(b)). The principal impact of this Final
Rule is: (1) elimination of certain requirements of 1.821 through
1.825; and (2) revision of 1.821 through 1.825 for consistency with
WIPO Standard ST.25 (1998), which will permit Sequence Listings to be
presented in an international, language neutral format.
The Office has determined that this Final Rule has no Federalism
implications affecting the relationship between the National Government
and the States as outlined in Executive Order 12612.
List of Subjects
37 CFR Part 1
Administrative practice and procedure, Courts, Freedom of Information,
Inventions and patents, Incorporation by reference, Reporting and
record-keeping requirements, Small businesses.
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For the reasons set forth in the preamble and under the authority
granted to the Commissioner of Patents and Trademarks by 35 U.S.C. 6,
Title 37 of the Code of Federal Regulations, part 1, is amended as
follows:
PART 1 - RULES OF PRACTICE IN PATENT CASES
1. The authority citation for 37 CFR part 1 continues to read as
follows: Authority: 35 U.S.C. 6, unless otherwise noted.
2. Section 1.821 is revised to read as follows:
1.821 Nucleotide and/or amino acid sequence disclosures in patent
applications.
(a) Nucleotide and/or amino acid sequences as used in 1.821 through
1.825 are interpreted to mean an unbranched sequence of four or more
amino acids or an unbranched sequence of ten 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 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
(1998), including Tables 1 through 6 in Appendix 2, herein incorporated
by reference. (Hereinafter "WIPO Standard ST.25 (1998)"). This
incorporation by reference was approved by the Director of the Federal
Register in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of
WIPO Standard ST.25 (1998) may be obtained from the World Intellectual
Property Organization; 34 chemin des Colombettes; 1211 Geneva 20
Switzerland. Copies of ST.25 may be inspected at the Patent Search Room;
Crystal Plaza 3, Lobby Level; 2021 South Clark Place; Arlington, VA
22202. Copies may also be inspected at the Office of the Federal
Register, 800 North Capitol Street, NW, Suite 700, Washington, DC.
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 WIPO
Standard ST.25 (1998), Appendix 2, Table 1.Modifications, e.g.,
methylated bases, may be described as set forth in WIPO Standard ST.25
(1998), Appendix 2, Table 2, 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 WIPO Standard ST.25
(1998), Appendix 2, Table 3. 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 WIPO Standard ST.25 (1998),
Appendix 2, Table 3 with the modified positions; e.g., hydroxylations or
glycosylations, being described as set forth in WIPO Standard ST.25
(1998), Appendix 2, Table 4, 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 WIPO Standard ST.25
(1998), Appendix 2, Table 3 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.
(b) Patent applications which contain disclosures of nucleotide and/or
amino acid sequences, in accordance with the definition in paragraph (a)
of this section, shall, with regard to the manner in which the
nucleotide and/or amino acid sequences are presented and described,
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conform exclusively to the requirements of 1.821 through 1.825.
(c) Patent applications which contain disclosures of nucleotide and/or
amino acid sequences must contain, as a separate part of the disclosure,
a paper copy disclosing the nucleotide and/or amino acid sequences and
associated information using the symbols and format in accordance with
the requirements of 1.822 and 1.823. This paper copy is hereinafter
referred to as the "Sequence Listing." Each sequence disclosed must
appear separately in the "Sequence Listing." Each sequence set forth in
the "Sequence Listing" shall be assigned a separate sequence identifier.
The sequence identifiers shall begin with 1 and increase sequentially by
integers. If no sequence is present for a sequence identifier, the code
"000" shall be used in place of the sequence. The response for the
numeric identifier <60> shall include the total number of SEQ ID NOs,
whether followed by a sequence or by the code "000."
(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 the sequence identifier, preceded by "SEQ ID NO:" in the text of
the description or claims, even if the sequence is also embedded in the
text of the description or claims of the patent application.
(e) A copy of the "Sequence Listing" referred to in paragraph (c) of
this section must also be submitted in computer readable form in
accordance with the requirements of 1.824.The computer readable form
is a copy of the "Sequence Listing" and will not necessarily be retained
as a part of the patent application file. If the computer readable form
of a new application is to be identical with the computer readable form
of another application of the applicant on file in the Patent and
Trademark Office, reference may be made to the other application and
computer readable form in lieu of filing a duplicate computer readable
form in the new application if the computer readable form in the other
application was compliant with all of the requirements of these rules.
The new application shall be accompanied by a letter making such
reference to the other application and computer readable form, both of
which shall be completely identified. In the new application, applicant
must also request the use of the compliant computer readable "Sequence
Listing" that is already on file for the other application and must
state that the paper copy of the "Sequence Listing" in the new
application is identical to the computer readable copy filed for the
other application.
(f) In addition to the paper copy required by paragraph (c) of this
section and the computer readable form required by paragraph (e) of this
section, a statement that the content of the paper and computer readable
copies are the same must be submitted with the computer readable form,
e.g., a statement that "the information recorded in computer readable
form is identical to the written sequence listing."
(g) If any of the requirements of paragraphs (b) through (f) 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,
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 submission in reply to a requirement under this
paragraph must be accompanied by a statement that the submission
includes no new matter.
(h) If any of the requirements of paragraphs (b) through (f) of this
section are not satisfied at the time of filing an international
application under the Patent Cooperation Treaty (PCT), which application
is to be searched by the United States International Searching Authority
or examined by the United States International Preliminary Examining
Authority, applicant will be sent a notice necessitating compliance with
the requirements within a prescribed time period. Any submission in
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reply to a requirement under this paragraph must be accompanied by a
statement that the submission does not include matter which goes beyond
the disclosure in the international application as filed. If applicant
fails to timely provide the required computer readable form, the United
States International Searching Authority shall search only to the extent
that a meaningful search can be performed without the computer readable
form and the United States International Preliminary Examining Authority
shall examine only to the extent that a meaningful examination can be
performed without the computer readable form.
3. Section 1.822 is revised to read as follows:
1.822 Symbols and format to be used for nucleotide and/or amino acid
sequence data.
(a) The symbols and format to be used for nucleotide and/or amino acid
sequence data shall conform to the requirements of paragraphs (b)
through (e) of this section.
(b) The code for representing the nucleotide and/or amino acid sequence
characters shall conform to the code set forth in the tables in WIPO
Standard ST.25 (1998), Appendix 2, Tables 1 and 3. This incorporation by
reference was approved by the Director of the Federal Register in
accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of ST.25 may
be obtained from the World Intellectual Property Organization; 34 chemin
des Colombettes; 1211 Geneva 20 Switzerland. Copies of ST.25 may be
inspected at the Patent Search Room; Crystal Plaza 3, Lobby Level; 2021
South Clark Place; Arlington, VA 22202. Copies may also be inspected at
the Office of the Federal Register, 800 North Capitol Street, NW, Suite
700, Washington, DC.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 WIPO Standard
ST.25 (1998), Appendix 2, Tables 2 and 4, and the modification is also
set forth in the Feature section. Otherwise, each occurrence of a base
or amino acid not appearing in WIPO Standard ST.25 (1998), Appendix 2,
Tables 1 and 3, shall be listed in a given sequence as "n" or "Xaa,"
respectively, with further information, as appropriate, given in the
Feature section, preferably by including one or more feature keys listed
in WIPO Standard ST.25 (1998), Appendix 2, Tables 5 and 6.
(c) Format representation of nucleotides:
(1) A nucleotide sequence shall be listed using the lower-case letter
for representing the one-letter code for the nucleotide bases set forth
in WIPO Standard ST.25 (1998), Appendix 2, Table 1.
(2) The bases in a nucleotide sequence (including introns) shall be
listed in groups of 10 bases except in the coding parts of the sequence.
Leftover bases, fewer than 10 in number, at the end of noncoding parts
of a sequence shall be grouped together and separated from adjacent
groups of 10 or 3 bases by a space.
(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 typed immediately
below the corresponding codons. Where a codon spans an intron, the amino
acid symbol shall be typed below the portion of the codon containing two
nucleotides.
(4) A nucleotide sequence shall be listed with a maximum of 16 codons or
60 bases per line, with a space provided between each codon or group of
10 bases.
(5) A nucleotide sequence shall be presented, only by a single strand,
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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 be
marked 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.
(7) For those nucleotide sequences that are circular in configuration,
the enumeration method set forth in paragraph (c)(6) of this section
remains applicable with the exception that the designation of the first
base of the nucleotide sequence may be made at the option of the
applicant.
(d) Representation of amino acids:
(1) The amino acids in a protein or peptide sequence shall be listed
using the three-letter abbreviation with the first letter as an upper
case character, as in WIPO Standard ST.25 (1998), Appendix 2, Table 3.
(2) A protein or peptide sequence shall be listed with a maximum of 16
amino acids per line, with a space provided between each amino acid.
(3) An amino acid sequence shall be presented in the amino to carboxy
direction, from left to right, and the amino and carboxy groups shall
not be presented 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 presented, 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. It shall be marked below the
sequence every 5 amino acids. 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 presented as separate amino acid
sequences.
(e) A sequence with a gap or gaps shall be presented as a plurality of
separate sequences, with separate sequence identifiers, with the number
of separate sequences being equal in number to the number of continuous
strings of sequence data. A sequence that is made up of one or more
noncontiguous segments of a larger sequence or segments from different
sequences shall be presented as a separate sequence.
4. Section 1.823 is revised to read as follows:
1.823 Requirements for nucleotide and/or amino acid sequences as part
of the application papers.
(a) The "Sequence Listing" required by 1.821(c), setting forth the
nucleotide and/or amino acid sequences and associated information in
accordance with paragraph (b) of this section, must begin on a new page
and must be titled "Sequence Listing". The "Sequence Listing" preferably
should be numbered independently of the numbering of the remainder of
the application. Each page of the "Sequence Listing" should contain no
more than 66 lines and each line should contain no more than 72
characters. A fixed-width font should be used exclusively throughout the
"Sequence Listing."
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(b) The "Sequence Listing" shall, except as otherwise indicated, include
the actual nucleotide and/or amino acid sequence, the numeric
identifiers and their accompanying information as shown in the following
table. The numeric identifier shall be used only in the "Sequence
Listing." The order and presentation of the items of information in the
"Sequence Listing" shall conform to the arrangement given below. Each
item of information shall begin on a new line and shall begin with the
numeric identifier enclosed in angle brackets as shown. 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. Numeric identifiers <110> through <170> shall only be set
forth at the beginning of the "Sequence Listing." The following table
illustrates the numeric identifiers.
Numeric Definition Comments and Mandatory (M) or
Identifier Format Optional (O)
<110> Applicant Preferably max. M
of 10 names;
one name per line;
preferable format:
Surname, Other
Names and/or
Initials
<120> Title of M
Invention
<130> File Reference Personal file M when filed prior
reference to assignment of
appl. number
<140> Current Applica- Specify as: M, if available
tion Number US 07/999,999 or
PCT/US96/99999
<141> Current Filing Specify as: yyyy-mm-dd M, if available
Date
<150> Prior Application Specify as: M, if applicable
Number US 07/999,999 or include priority
PCT/US96/99999 documents under
35 USC 119 and
120
<151> Prior Application Specify as: yyyy-mm-dd M, if applicable
Filing Date
<160> Number of SEQ ID Count includes M
NOs total number of
SEQ ID NOs
<170> Software Name of software used O
to create the
Sequence Listing
<210> SEQ ID NO:#: Response shall be an M
integer repre-
senting the SEQ
ID NO shown
<211> Length Respond with an integer M
expressing the number
of bases or amino acid
residues
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<212> Type Whether presented M
sequence mole-
cule is DNA,
RNA, or PRT
(protein). If
a nucleotide
sequence con-
tains both DNA
and RNA frag-
ments, the
type shall be
"DNA." In ad-
dition, the
combined DNA/
RNA molecule
shall be further
described in
the <220> to
<223> feature
section.
<213> Organism Scientific name, M
i.e. Genus/species,
Unknown or Artifi-
cial Sequence. In
addition, the
"Unknown" or
"Artificial Se-
quence" organisms
shall be further
described in the
<220> to <223>
feature section.
<220> Feature Leave blank after M, under the
<220>. <221-223> following condi-
provide for a tions: if "n,"
description of "Xaa," or a mod-
points of bio- ified or unusual
logical signi- L-amino acid or
ficance in the modified base was
sequence. used in a se-
quence; if ORGAN-
ISM is "Artifi-
cial Sequence" or
"Unknown"; if
molecule is
combined DNA/RNA.
<221> Name/Key Provide appropriate M, under the fol-
identifier for lowing conditions:
feature, pre- if "n," "Xaa," or
ferably from a modified or un-
WIPO Standard usual L-amino
ST.25 (1998), acid or modified
Appendix 2, base was used in
Tables 5 and 6 a sequence
<222> Location Specify location M, under the fol-
within sequence; lowing conditions:
where appropriate if "n," "Xaa," or
state number of a modified or un-
first and last usual L-amino
bases/amino acids acid or modified
in feature base was used in
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a sequence
<223> Other Infor- Other relevant M, under the fol-
mation information; lowing conditions:
four lines maximum if "n," "Xaa," or
a modified or un-
usual L-amino acid
or modified base
was used in a
sequence; if
ORGANISM
is "Artificial
Sequence" or
"Unknown"; if
molecule is com-
bined DNA/RNA.
<300> Publication Leave blank O
Information after <300>
<301> Authors Preferably max O
of ten named
authors of publi-
cation; specify
one name per line;
preferable format:
Surname, Other
Names and/or
Initials
<302> Title O
<303> Journal O
<304> Volume O
<305> Issue O
<306> Pages O
<307> Date Journal date on which O
data published;
specify as yyyy-mm-
dd, MMM-yyyy or
Season-yyyy
<308> Database Accession number O
Accession assigned by data-
Number base including
database name
<309> Database Entry Date of entry in O
Date database; specify
as yyyy-mm-dd or
MMM-yyyy
<310> Patent Document Document number; O
Number for patent-type
citations only.
Specify as, for
example, US
07/999,999
<311> Patent Filing Document filing O
Date date, for patent-
type citations only;
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specify as yyyy-mm-dd
<312> Publication Date Document publication O
date, for
patent-type
citations only;
specify as yyyy-mm-dd
<313> Relevant FROM (position) TO O
Residues (position)
<400> Sequence SEQ ID NO should M
follow the
numeric identifier
and should appear
on the line pre-
ceding the actual
sequence
5. Section 1.824 is revised to read as follows:
1.824 Form and format for nucleotide and/or amino acid sequence
submissions in computer readable form.
(a) The computer readable form required by 1.821(e) shall meet the
following specifications:
(1) The computer readable form shall contain a single "Sequence Listing"
as either a diskette, series of diskettes, or other permissible media
outlined in paragraph (c) of this section.
(2) The "Sequence Listing" in paragraph (a) (l) of this section shall be
submitted in American Standard Code for Information Interchange (ASCII)
text. No other formats shall be allowed.
(3) The computer readable form may be created by any means, such as word
processors, nucleotide/amino acid sequence editors or other custom
computer programs; however, it shall conform to all specifications
detailed in this section.
(4) File compression is acceptable when using diskette media, so long as
the compressed file is in a self-extracting format that will decompress
on one of the systems described in paragraph (b) of this section.
(5) Page numbering shall not appear within the computer readable form
version of the "Sequence Listing" file.
(6) All computer readable forms shall have a label permanently affixed
thereto on which has been hand-printed or typed: the name of the
applicant, the title of the invention, the date on which the data were
recorded on the computer readable form, the operating system used, a
reference number, and an application serial number and filing date, if
known.
(b) Computer readable form submissions must meet these format
requirements:
(1) Computer: IBM PC/XT/AT, or compatibles, or Apple Macintosh;
(2) Operating System: MS-DOS, Unix or Macintosh;
(3) Line Terminator: ASCII Carriage Return plus ASCII Line Feed;
(4) Pagination: Continuous file (no "hard page break" codes permitted);
(c) Computer readable form files submitted may be in any of the
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following media:
(1) Diskette:
3.50 inch, 1.44 Mb storage;
3.50 inch, 720 Kb storage;
5.25 inch, 1.2 Mb storage;
5.25 inch, 360 Kb storage.
(2) Magnetic tape:
0.5 inch, up to 24000 feet;
Density: 1600 or 6250 bits per inch, 9 track;
Format: Unix tar command; specify blocking factor (not
"block size");
Line Terminator: ASCII Carriage Return plus ASCII
Line Feed.
(3) 8mm Data Cartridge:
Format: Unix tar command; specify blocking factor (not
"block size");
Line Terminator: ASCII Carriage Return plus ASCII
Line Feed.
(4) CD-ROM:
Format: ISO 9660 or High Sierra Format
(5) Magneto Optical Disk:
Size/Storage Specifications: 5.25 inch, 640 Mb.
(d) Computer readable forms that are submitted to the Office will not be
returned to the applicant.
6. Section 1.825 is revised to read as follows:
1.825 Amendments to or replacement of sequence listing and computer
readable copy thereof.
(a) Any amendment to the paper copy of the "Sequence Listing" (
1.821(c)) must be made by the submission of substitute sheets.
Amendments must be accompanied by a statement that indicates support for
the amendment in the application, as filed, and a statement that the
substitute sheets include no new matter.
(b) Any amendment to the paper copy of the "Sequence Listing," in
accordance with paragraph (a) of this section, must be accompanied by a
substitute copy of the computer readable form ( 1.821(e)) including
all previously submitted data with the amendment incorporated therein,
accompanied by a statement that the copy in computer readable form is
the same as the substitute copy of the "Sequence Listing."
(c) Any appropriate amendments to the "Sequence Listing" in a patent;
e.g., by reason of reissue or certificate of correction, must comply
with the requirements of paragraphs (a) and (b) of this section.
(d) If, upon receipt, the computer readable form is found to be damaged
or unreadable, applicant must provide, within such time as set by the
Commissioner, a substitute copy of the data in computer readable form
accompanied by a statement that the substitute data is identical to that
originally filed.
7. Appendix A to Subpart G to Part 1 is revised to read as follows:
Appendix A To Subpart G to Part 1 - Sample Sequence Listing
<110> Smith, John
Smith, Jane
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US PATENT AND TRADEMARK OFFICE |
1397 CNOG 657 |
<120> Example of a Sequence Listing
<130> 01-00001
<140> US 08/999,999
<141> 1998-02-28
<150> EP 91000000
<151> 1997-12-31
<160> 2
<170> PatentIn ver. 2.0
<210> 1
<211> 403
<212> DNA
<213> Paramecium aurelia
<220>
<221> CDS
<222> 341..394
<300>
<301> Doe, Richard
<302> Isolation and Characterization of a Gene Encoding a
Protease from Paramecium sp.
<303> Journal of Fictional Genes
<304> 1
<305> 4
<306> 1 - 7
<307> 1988-06-20
<400> 1
ctactctact ctactctcat ctactatctt ctttggatct ctgagtctgc ctgagtggta 60
ctcttgagtc ctggagatct ctcctctcac atgtgatcgt cgagactgac cgatagatcg 120
ctgactgact ctgagatagt cgagcccgta cgagacccgt cgagggtgac agagagtggg 180
cgcgtgcgcg cagagcgccg cgccggtgcg cgcgcgagtg cgcggtgggc cgcgcgaggg 240
ctttcgcggc agcggcggcg ctttccggcg cgcgcccgtc cgcccctaga cctgagaggt 300
cttctcttcc ctcctcttca ctagagaggt ctatatatac atg gtt tca atg ttc 355
Met Val Ser Met Phe
1 5
agc ttg tct ttc aaa tgg cct gga ttt tgt ttg ttt gtt tgtttg 403
Ser Leu Ser Phe Lys Trp Pro Gly Phe Cys Leu Phe Val
10 15
<210> 2
<211> 18
<212> PRT
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US PATENT AND TRADEMARK OFFICE |
1397 CNOG 658 |
<213> Paramecium aurelia
<400> 2
Met Val Ser Met Phe Ser Leu Ser Phe Lys Trp Pro Gly Phe Cys Leu
1 5 10 15
Phe Val
May 22, 1998 BRUCE A. LEHMAN
Assistant Secretary of Commerce and
Commissioner of Patents and Trademarks
[1211 OG 82]