WIPO Sequence Listings Standards for PCT Applications

Just like each and every aspect of a patent application is crucial, sequence listing is equally an indispensable part of it. Sequence listings become a part of your biological patents where amino acid and nucleotide sequences disclosure is mandatory. Indeed there are certain standards for filing sequence listings in both national and international applications.

Here through this article we are going to discuss the international standards of sequence listings for creating an up-to-the-mark patent application. This includes the WIPO approved standards for PCT applications.

Also, read PCT Patent Filing: All That You Need to Know, if you want to file an international patent application through PCT mode.

Additionally, you will find the correct symbols, format and presentation of the sequences (amino acids and nucleotide) which are acceptable by the patent offices, International Searching and Preliminary Examination Authorities.

Symbols and Format for Nucleotide Sequence Listings

Symbols are the abbreviated representations of the bases that make up a nucleotide sequence. While the format of sequence listings is how you represent the amino acid and nucleotide bases in the list.

“Symbols” for Nucleotide Sequences:

  • Represent the bases of a nucleotide sequence by using the one-letter code for nucleotide sequence characters. Also, identify those sequences by lower case characters.
  • Modifications in the bases by the corresponding unmodified bases or as “n” in the sequence itself. These codes may be used in the description or the feature section of the sequence listing but not in the sequence itself. The symbol “n” is the equivalent of only one unknown or modified nucleotide.
Nucleotide Symbols
Figure 1. Symbols for Nucleotide Sequences

“Format” for Nucleotide Sequences:

  • A nucleotide sequence shall contain a maximum of 60 bases per line, with a space between each group of 10 bases.
  • The bases of 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 numbers at the end of noncoding parts of a sequence, should be grouped together and separated from adjacent groups by a space.
  •  List the bases of the coding parts of a nucleotide sequence as triplets (codons).
  • Present the nucleotide sequence only by a single strand, in the 5’-end to 3’-end direction from left to right in a continuous fashion. The terms 3’ and 5’ shall not be represented in the sequence.
  • It 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. The enumeration method for nucleotide sequences applies to nucleotide sequences that are circular in configuration as well.
  • Prepare a separate sequence if there is a nucleotide sequence that is made up of one or more non-contiguous segments of a larger sequence or of segments from different sequences. Mark them with a separate sequence identifier.
  • Moreover, if there is a sequence with a gap or gaps then number them as a plurality of separate sequences with separate sequence identifiers.
Nucleotide Sequence Listings Example


Figure 2. Nucleotide Sequence Listings Example

Symbols and Format for Amino Acid Sequence Listings

For amino acid sequences the rules are somewhat the same as nucleotide sequences but with a few differences which are specific to amino acid structures.

Amino acid symbols
Figure 3. Amino Acid Symbols for Sequence Listings

“Symbols” for Amino Acid Sequences:

  • Represent the amino acids using the three-letter code with the first letter as capital.
  • An amino acid sequence that contains a blank or internal terminator symbols (for example, “Ter” or “*” or “.”) may not be represented as a single amino acid sequence, but shall be presented as separate amino acid sequences.
  • Represent modified and unusual amino acids as “Xaa” in the sequence itself. Also, provide a description of modification in the feature section of the sequence listing using codes. Moreover, these codes are a part of the description or the feature section of the sequence listing but not in the sequence itself. The symbol “Xaa” is the equivalent of only one unknown or modified amino acid.

“Format” for Amino Acid Sequences:

  • The representation of amino acids in a protein or peptide sequence is from amino to carboxy direction from left to right. But, there is no representation of amino and carboxy groups in the sequence.
  • There are a maximum of 16 amino acid per line for each protein or peptide sequence with space provided between each amino acid.
  • Amino acids corresponding to the codons in the coding parts of a nucleotide sequence shall be placed immediately under the corresponding codons.
  • The enumeration of amino acids shall start at the first amino acid of the sequence, with number 1.
  • Adding on to the complexity of amino acids, the amino acids preceding the mature protein, for example pre-sequences, pro-sequences, pre-pro-sequences and signal sequences, when present, may have negative numbers, counting backwards starting with the amino acid next to number 1.
  • Furthermore, if there is an amino acid sequence that is made up of one or more non-contiguous segments of a larger sequence or of segments from different sequences then number those sequences separately with a separate sequence identifier. Moreover, if there is a sequence with a gap or gaps then number them as a plurality of separate sequences with separate sequence identifiers.

Prepare Sequence Listings with The Sequence Listing Company

By now you understand that sequence listings play a vital role for getting your biological invention through the examination of the patent office. Also, there are multiple rules to be strictly followed to prepare standardized sequence listings.

Our professionals hold years of experience preparing sequence listings as per the standards set by WIPO, USPTO and other patent offices. With this comes the knowledge of handling the technicalities while preparing the structured lists. We have command over some of the state-of-the-art tools like PatentIn 3.5 and BiSSAP. For us customer satisfaction is of utmost importance and therefore we offer a quick turn-around-time and timely delivery of results.

In order to avail our services, visit The Sequence Listing Company service page.

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