1. Multiple sources: All nucleotide and amino acid sequences require a “source” functional key that spans the entire sequence, with a mandatory “organism” qualifier. Sequences from multiple sources can be further described with the feature key “misc_feature” and the qualifier “note” for nucleotide sequencesas well as the function key “REGION” and the qualifier “note” for amino acid sequences.
2. Mol_type qualifier: The mandatory source function key also requires a mol_type qualifier to further describe the molecule.
- The “mol_type” qualifier value is “protein” for amino acid sequences.
- The mol_type qualification value for DNA sequences can be genomic DNA, other DNA, or unassigned DNA. The value “genomic DNA” does not imply that the molecule is nuclear (eg, organelle and plasmid DNA must be described with “genomic DNA”).
- The mol_type qualification value for RNA sequences can be genomic RNA, mRNA, tRNA, rRNA, other RNA, transcribed RNA, viral cRNA, or unassigned RNA. Note that ribosomal RNA genes must be described with “genomic DNA”; “rRNA” may only be used if the ribosomal RNA molecule itself has been sequenced.
- Use the qualifier value “other DNA/RNA” for synthetic DNA/RNA molecules.
- Use the unassigned DNA/RNA qualifier value when the in vivo DNA/RNA molecule is unknown.
3. File number of the applicant: It is necessary to update the “Applicant’s reference number” in an ST.26 sequence listing in XML format for each US serial or divisional application. The USPTO uses this information to match the sequence listing to the correct application.
4. Application number: It is mandatory to include the application number in an ST.26 sequence listing XML if one has already been assigned. Even if the box “Before assigning the application number” is ticked and the mandatory “Applicant’s reference number” is included, the validation in the WIPO sequence will issue the following WARNING: “No application information has been entered. If the application number has been assigned, it must be entered.” If the application number has not yet been assigned, this WARNING can be ignored.
5. Qualifier ID Numbers: A bug in the current version of the WIPO sequence (version 2.1.2) updates the identifier ID numbers (qID) when importing an ST.26 sequence listing. qID numbers are not required to be sequential or in any particular order, but each qID must be unique. When this happens and all qID numbers are unique, the import report messages stating “The identifier ID has been updated because the specified value is already taken” may be ignored.
6. Importing general information: In the current version of the WIPO sequence (version 2.1.2), when importing a sequence listing, general information will not be imported without the “Select the general information content to import” box (see below) being checked. The box to the left of “Element” must also be checked in order to import all general information. To import only certain general information items, simply uncheck the box to the left of “Item” and check the box next to each item you want to import. Conversely, all sequences will be imported regardless of whether or not the “Enter the sequences to import” checkbox (see below) is checked.