2429 Helpful Hints for Compliance [R-08.2012]
The Office has now had a good deal of experience in the implementation of the sequence rules. The following list sets forth helpful hints, for both examiners and applicants, for compliance. For the most part, the list is a compilation of frequently asked questions.
—Compliance is not a filing date issue.
—Compliance is not a 35 U.S.C. 112 issue.
—Compliance is not a 35 U.S.C. 119/120 issue.
—Compliance is not per se a new matter issue. The standard for resolution of inconsistencies between the official “Sequence Listing” (submitted on paper or compact disc pursuant to 37 CFR 1.821(c)) and the computer readable form thereof and/or errors in the official copy of sequence information is based on the new matter standard. If there are inconsistencies in compact discs submitted in accordance with 37 CFR 1.52(e) between “Copy 1” and “Copy 2”, the compact disc labeled “Copy 1” will be used for further processing.
—Compliance can be achieved via amendment.
—The paper or compact disc copy of the Sequence Listing is an integral part of the application. If submitted on paper, the Sequence Listing must begin on a new page, should appear at the end of the application, and preferably should be numbered independently of the numbering of the remainder of the application. The new page that begins the “Sequence Listing” should be entitled “Sequence Listing.” If not submitted as such at filing, the Sequence Listing must be inserted into the application via amendment, e.g., by preliminary amendment. If submitted on compact disc, the specification must contain an incorporation by reference of the material on the compact disc in a separate paragraph identifying each compact disc.
—Substitute pages or replacement compact discs must be used for changes to the Sequence Listing for each respective format.
—Angle brackets and numeric identifiers listed in 37 CFR 1.823 are very important for our database. Extra punctuation should not be used in Sequence Listings.
—The computer readable form cannot contain page numbers. Page numbers should only be placed on the paper copy of the Sequence Listing. Page numbers should not be placed on the compact disc copy of the Sequence Listing.
—The PatentIn computer program is not the only means by which to comply with the rules. Any word processing program can be used to generate a Sequence Listing if it has the capability to convert a file into ASCII text.
—If a word processing program is used to generate a “Sequence Listing,” hard page break controls should not be used and margins should be adjusted to the smallest setting.
—Word processing files should not be submitted to the Office; the Sequence Listing generated by a word processing file should be saved as an ASCII text file for submission. Most word processing programs provide this feature.
—Statements in accordance with 37 CFR 1.821(f), (g), (h) and 37 CFR 1.825 and proper labeling in accordance with 37 CFR 1.824(a)(6) should be noted. Sample statements to support filings and submissions in accordance with 37 CFR 1.821 through 1.825 are provided in MPEP § 2428 Sample Statements.
—Use Box SEQUENCE.
—Three and a half inch disks are less fragile than five and a quarter inch disks.
—On nucleotide sequences, since only single strands may be depicted in the “Sequence Listing,” show strands in 5′ to 3′ direction.
—The single stranded nucleotide depicted in the “Sequence Listing” may represent a strand of a nucleotide sequence that may be single or double stranded which may be, further, linear or circular. An amino acid sequence or peptide may be linear or circular. In some instances, a sequence may be both single stranded and double stranded and/or both linear and circular. The response “not relevant” is also an acceptable response for both “Strandedness” and “Topology.”
—Numeric identifiers “<140>, Current Application Number,” “<141>, Current Filing Date,” “<150>, Prior Application Number,” and “<151>, Prior Application Filing Date,” should appear in the “Sequence Listing” in all cases. If the information about the current application is not known or is unavailable at the time of completing the Sequence Listing, then the lines following numeric identifiers <140> and <141> should be left blank. This would normally be the case when the “Sequence Listing” is included in a newly filed application. Similarly, if information regarding prior applications is inapplicable, or not known at the time of completing the “Sequence Listing” but will be later filed, then the numeric identifiers <150> and <151> should appear with the line following the numeric identifiers left blank.
—If you receive a Notice to Comply that should not have been sent to you, send a letter in the form of a request for reconsideration of the notice to the organization sending the notice.
—There are a limited number of mandatory items of information. They are identified in MPEP § 2424.02 Sequence Listing Numeric Identifiers.
—Figures can be used to convey information not readily conveyed by the Sequence Listing. The exclusive conformance requirement of 37 CFR 1.821(b) will be relaxed for drawing figures. However, the sequence information so conveyed must still be included in a “Sequence Listing” and the sequence identifier (“SEQ ID NO:X”) must be used, either in the drawing or in the “Brief Description of the Drawings.”
—Extra copies of computer readable forms should not be sent to examiners.
—Inosine may be represented by the use of “I” in the features section, otherwise use “n.”
—Stop codons, represented by an asterisk, are not permitted in amino acid sequences.
—Punctuation should not be used in a sequence to indicate unknown nucleotide bases or amino acid residues nor should punctuation be used to delimit active or functional regions of a sequence. These regions should be noted as Features of the sequence per 37 CFR 1.823(b) (see numeric identifiers <220> - <223>.
—The presence of an unnatural amino acid in a sequence does not have the same effect as the presence of a D-amino acid. The sequence may still be subject to the rules even though one or more of the amino acids is not naturally occurring.
—Cyclic and branched peptides are causing some confusion in the application of the rules. Specific questions should be directed to Group 1650 personnel.
—A cyclic peptide with a tail is regarded as a branched sequence, and thereby exempt from the rules, if all bonds adjacent to the amino acid from which the tail emanates are normal peptide bonds.
—Sequences that have variable-length regions depicted as, for example, Ala Ala Leu Leu (Xaa Xaa)n Ile Pro where n=0-234 or agccttgggaca(nnnnn)mgtcatt where m=0-354 or Ser Met Ala Xaa Ser where Xaa could be 1, 2, 3, 4 and/or 5 amino acids must still comply with the Sequence Rules. The method to use is to repeat the variable-length region as many times as the maximum length and specify in the Features section that the amino acid (or nucleotide) at a specified position is either absent or present. The variables Xaa and n may stand for only one residue, hence the need to repeat the variable. The correct way to submit the third example is Ser Met Ala Xaa Xaa Xaa Xaa Xaa Ser combined with an explanation in the Features section of the listing that any one or all of amino acids 4-8 can either be present or absent.
—Single letter amino acid abbreviations are not acceptable within the Sequence Listing but may appear elsewhere in the application.
—Zero (0) is not used when the numbering of amino acids uses negative numbers to distinguish the mature protein.
—Subscripts or superscripts are not permitted in a Sequence Listing.
—If a “Sequence Listing” is amended, an entirely new computer readable form is required regardless of the triviality of the amendment. Amendments to the paper copy of the “Sequence Listing” must be made by replacement section in compliance with 37 CFR 1.121. Amendments to the compact disc copy of the “Sequence Listing” must be made by replacement discs.
—Note field length limitations. For specific instances, they may be waived, but compliance is encouraged.
—The exclusive conformance requirement of 37 CFR 1.821(b) requires that any amendment of the sequence information in a “Sequence Listing” be accompanied by an amendment to the corresponding information, if any, embedded in the text of the specification or presented in a drawing figure.
—Any inquiries regarding a specific computer readable form that has been processed by the Office should be directed to the Systems Branch of the Chemical/Biotechnology Division of the Scientific and Technical Information Center.