WIPO ST.26 Breakdown - Part IV

As we continue to work our way through the "representation of sequences" section, the focus remains on nucleotide sequences, specifically the complicated concepts of modified nucleotides. The first item discussed is that any "ambiguity symbol" (n, m, r, w, s, y, k, v, h, d or b) must be included as the most concise option. For example, a position that may be "a" or "g" must be included as an "r" rather than an "n". The symbol "n" is always interpreted as "a", "c", "g" or "t/u" unless further defined in a feature table. "n" can also only be a nucleotide and each "n" represents a single nucleotide.

It is important to note that if "n" represents "a", "c", "g" or "t/u" no features or qualifiers are required in the feature table. This differs from ST.25 which requires a "modified_base" feature with a description in the <223> line for all "n" positions regardless of if it is a standard "a", "c", "g" or "t/u."

Getting even more complicated, we begin to dive into the language surrounding modified nucleotides. ST.26 states: "A modified nucleotide must be further described in the feature table…using the feature key “modified_base” and the mandatory qualifier “mod_base” in conjunction with a single abbreviation from Annex I (see Section 2, Table 2) as the qualifier value; if the abbreviation is “OTHER”, the complete unabbreviated name of the modified nucleotide must be provided as the value in a “note” qualifier. For a listing of alternative modified nucleotides, the qualifier value “OTHER” may be used in conjunction with a further “note” qualifier (see paragraphs 97 and 98).”

The requirements for modification above are much more complicated than WIPO ST.25 as it requires the applicant to understand and be aware of the modifications in Section 2, Table 2 rather than being able to account for all modifications in the same manner. If the modification is known and described with an abbreviation in Table 2, it must be abbreviated in the listing. If the modification is not in Table 2 it must be described with a full unabbreviated name. In theory, it makes sense to standardize common modifications utilize their abbreviations, however, it is also known that sequence disclosures in patent applications are wildly inconsistent which may make the application of this rule complicated.

With about 3 months left before the implementation of ST.26, please contact me if you have any questions.