For the final post in our Big Bang Blog Series we wanted to share some tips that you will find helpful during the sequencing and filing process. Tune back in for more updates as the WIPO Standard evolves.
1. Multiple sources: All nucleotide and amino acid sequences require a “source” feature key spanning the entirety of the sequence with a mandatory “organism” qualifier. Sequences from multiple sources may be further described using the feature key “misc_feature” and the qualifier “note” for nucleotide sequences, and the feature key “REGION” and the qualifier “note” for amino acid sequences.
2. “mol_type” qualifier: The mandatory “source” feature 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” qualifier 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 (e.g., organelle and plasmid DNA must be described using “genomic DNA”).
- The “mol_type” qualifier value for RNA sequences can be “genomic RNA”, “mRNA”, “tRNA”, “rRNA”, “other RNA”, “transcribed RNA”, “viral cRNA”, or “unassigned RNA”. Note ribosomal RNA genes must be described using “genomic DNA”; “rRNA” must 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 qualifier value “unassigned DNA/RNA” when the in vivo DNA/RNA molecule is unknown.
3. Applicant file reference: It is necessary to update the “applicant file reference” number in an ST.26 sequence listing XML for each U.S. continuation 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 “Before the assignment of the application number” box is checked and the mandatory “Applicant file reference” is included, validation in WIPO Sequence will issue the following WARNING: “An application identification information has not been entered. If the application number has been assigned, it must be entered.” If the application number has not yet been assigned, this WARNING may be ignored.
5. Qualifier ID numbers: A bug in the current version of WIPO Sequence (version 2.1.2) will update qualifier ID (qID) numbers upon import of an ST.26 sequence listing. It is not required that qID numbers are consecutive or in a particular order, but each qID must be unique. If this happens, and all qID numbers are unique, the import report messages reading “The qualifier ID has been updated as the specified value was already taken” may be ignored.
6. Importing of general information: In the current version of WIPO Sequence (version 2.1.2), when importing a sequence listing, general information will not be imported without checking the “Select the general information contents to be imported” box (see below). The box to the left of “Element” must also be checked to import all general information. To only import certain general information elements, simply uncheck the box to the left of “Element” and check the box next to each element to be imported. Conversely, all sequences will be imported whether the “Enter the sequences to be imported” box (see below) is checked or not.