How are modified amino acids represented in a sequence listing?

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.

According to MPEP 2412.05(d), modified amino acids should be represented as follows:

• Represent as the corresponding unmodified amino acid when possible
• Use ‘X’ for modified amino acids that cannot be represented by other symbols
• Provide further description in a feature table

The MPEP states, “WIPO Standard ST.26, paragraph 29, specifies that modified amino acids, including D-amino acids, should be represented in the sequence as the corresponding unmodified amino acids whenever possible. Any modified amino acid in a sequence that cannot otherwise be represented by any other symbol in Table 3: List of Amino Acids Symbols (reproduced in MPEP § 2412.03(a)), i.e., an “other” amino acid, must be represented by “X”.” Additionally, modified amino acids must be further described in a feature table using appropriate feature keys and qualifiers.