Amino acid or nucleic acid sequences can be defined by a percentage of identity. The percentage of identity determines the number of identical residues over a defined length in a given alignment. If no algorithm or calculation method for determining the percentage of identity is defined, the broadest interpretation will be applied using any reasonable algorithm or calculation method known at the relevant filing date.
Amino acid sequences can be defined by a degree of similarity (expressed as a percentage of similarity). The term similarity is broader than the term identity because it allows conservative substitutions of amino acid residues having similar physicochemical properties over a defined length of a given alignment. The percentage of similarity is determinable only if a similarity-scoring matrix is defined. If no similarity-scoring matrix is defined, a claim referring to a sequence displaying a percentage of similarity to a recited sequence is considered to cover any sequence fulfilling the similarity requirement as determined with any reasonable similarity-scoring matrix known at the relevant filing date.
For amino acid sequences, if a percentage of homology is used by the applicant as the only feature to distinguish the subject-matter of a claim from the prior art, its use is objected to under Art. 84 (cf. F‑IV, 4.6.1) unless the determination or calculation of the percentage of homology is clearly defined in the application as filed. For nucleic acid sequences, homology percentage and identity percentage are usually considered to have the same meaning.