uspto.gov
Skip over navigation

2423    Symbols and Format To Be Used for Nucleotide and/or Amino Acid Sequence Data [R-08.2012]

37 C.F.R. 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, 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.

Tables 1-6 of WIPO Standard ST.25 (1998), Appendix 2, are reproduced in MPEP § 2422.

2423.01   Format and Symbols To Be Used in Sequence Listings [R-08.2012]

37 CFR 1.822 sets forth the format and symbols to be used for listing nucleotide and/or amino acid sequence data. The codes for representing the nucleotide and/or amino acid characters in the sequences are set forth in the tables of WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3. See MPEP § 2422. No other symbols shall be used in nucleotide and amino acid sequences. The “modified base” and “modified and unusual amino acid” codes appearing in WIPO Standard ST.25 (1998), Appendix 2, Tables 2 and 4 (see 37 CFR 1.822 and MPEP § 2422) are not to be set forth in the sequences recited in the Sequence Listing. However, “modified base” or “modified and unusual amino acid” codes may be used in the written description and/or drawing portions of the specification. To properly enter notations for modified codes in the Sequence Listing, the Feature section of the Sequence Listing should be used. That is, a modified base or amino acid may be presented in a given sequence as the corresponding unmodified base or amino acid if the modified base or amino acid is one of those listed in WIPO Standard ST.25 (1998), Appendix 2, Table 2 or 4 and the modification is also set forth in the Feature section of the Sequence Listing. Otherwise, all bases or amino acids not appearing in WIPO Standard ST.25 (1998), Appendix 2, Table 1 or 3 must be listed in a given sequence as “n” or “Xaa,” respectively, with further information given in the Feature section of the “Sequence Listing.” See 37 CFR 1.823(b).

In 37 CFR 1.822(b) and 37 CFR 1.822(d), the use of three-letter codes for amino acids is required. The use of the three-letter codes for amino acids is preferred over the one-letter codes from the perspective of facilitating the examiner’s review of the application papers, including the “Sequence Listing”, and the public’s, as well as the examiner’s, use of the printed patents. The three-letter codes must be presented using the upper case for the first character and lower case for the remaining two characters.

37 CFR 1.822(c) through (e) set forth the format for presenting sequence data. These paragraphs set forth the manner in which the characters in sequences are to be grouped, spaced, presented and numbered.

2423.02   Depiction of Coding Regions [R-08.2012]

If applicant chooses to depict coding regions, 37 CFR 1.822(c)(3) requires the amino acids corresponding to the codons in the coding parts of a nucleotide sequence to be typed immediately below the corresponding codons. Further, in 37 CFR 1.822(c)(3), the situation in which a codon spans an intron has been addressed. In those situations, the “amino acid symbol shall be typed below the portion of the codon containing two nucleotides.” This requirement clarifies the representation of an amino acid that corresponds to a codon that spans an intron.

It should be noted that the sequence rules do not, in any way, require the depiction of coding regions or the amino acids corresponding to the codons in those coding regions. 37 CFR 1.822(d) only requires that where amino acids corresponding to the codons in the coding parts of a nucleotide sequence are depicted, they must be depicted below the corresponding codons. There is absolutely no requirement in the rules to depict coding regions. Nor is there a requirement to separately list the amino acids corresponding to the codons in the coding parts of a nucleotide sequence unless the applicant desires to discuss the amino acids as a separate sequence. That is, when the coding parts of a nucleotide sequence and their corresponding amino acids have been identified, if applicant desires to discuss those amino acids in the coding parts of the nucleotide as a separate sequence, those amino acids must also be set forth as a separate sequence. The separate submission of the amino acid sequence that corresponds to the coding parts of a nucleotide sequence is, however, recommended and encouraged because the amino acid sequence may not be captured in the sequence database if it is only presented in the “Sequence Listing” as a mixed nucleotide and amino acid sequence.

2423.03   Presentation and Enumeration of Sequences [R-08.2012]

37 CFR 1.822(c)(5) provides that nucleotide sequences shall only be represented by a single strand, in the 5′ to 3′ direction, from left to right. That is, double stranded nucleotides shall not be represented in the “Sequence Listing.” A double stranded nucleotide may be represented as two single stranded nucleotides, and any relationship between the two may be shown in the drawings.

The procedures for presenting and numbering amino acid sequences are set forth in 37 CFR 1.822(d). Two alternatives are presented for numbering amino acid sequences. Amino acid sequences may be numbered with respect to the identification of the first amino acid of the first mature protein or with respect to the first amino acid appearing at the amino terminal. The enumeration procedure for nucleotides is set forth in 37 CFR 1.822(c)(6). Sequences that are circular in configuration are intended to be encompassed by these rules, and numbering procedures for them are provided in 37 CFR 1.822(c)(7) and (d)(4). The numbering procedures set forth in 37 CFR 1.822(c) and (d) are not necessarily intended to be consistent with all currently employed numbering procedures. The objective here is to establish a reasonable numbering procedure that can readily be followed and adhered to. These formatting procedures also reflect those that have been agreed to for electronic data exchange with the JPO and the EPO.

In 37 CFR 1.822(e) the procedures for presenting and numbering hybrid and gapped sequences are set forth. A sequence that is made up of one or more noncontiguous segments of a larger sequence or segments from different sequences, i.e., a hybrid sequence, shall be presented as a separate sequence. A “gap” for the purpose of this section is not intended to embrace a gap or gaps that is/are introduced into the presentation of otherwise continuous sequence information in, e.g., a drawing figure, to show alignments or similarities with other sequences. The “gaps” referred to in this section are gaps representing unknown or undisclosed regions in a sequence between regions that are known or disclosed. In the situation where a contiguous fragment of a sequence that has already been properly set forth in a “Sequence Listing” is discussed and/or claimed, the fragment does not need to be separately included in the “Sequence Listing.” It may be referred to in the specification, claims or drawings as, e.g., “residues 2 through 33 of SEQ ID NO:12,” assuming that SEQ ID NO:12 has been properly included in the “Sequence Listing.”

[top]

 

United States Patent and Trademark Office
This page is owned by Patents.
Last Modified: 03/27/2014 10:10:34