How should modified residues be represented in a Sequence Listing XML?

This page is an FAQ based on guidance from the Manual of Patent Examining Procedure. It is provided as guidance, with links to the ground truth sources. This is information only: it is not legal advice.

Representing modified residues correctly in a Sequence Listing XML is crucial for accurately describing non-standard amino acids or nucleotides. According to MPEP 2413.01(g):

“For the ‘note’ qualifier, where the variant residue is a modified residue not set forth in Table 2, the complete unabbreviated name of the modified residue must be provided as the qualifier value. Modified residues must be further described in a FEATURE TABLE as described above at subsection (I).”

Key points for representing modified residues:

• Use the appropriate symbols from Tables 1 to 3 where possible.
• For modified residues not in these tables, provide the full, unabbreviated name in the “note” qualifier.
• Include additional description in the feature table for clarity.

Proper representation of modified residues ensures that all relevant structural information is accurately captured in the patent application.