Algorithm for the identical match ratio calculation between conserved proteins. (A) Alignment output of Protein-BLAST. The colored box shows a conserved region between query and subject sequences defined by BLAST. Match type i and h indicate identical matches and homologous substitutions, which are based on the BLOSUM62 matrix, and - means no similarity or a gap. (B) The equation used to calculate the identical match ratio. A large substitution ratio within a conserved region leads to a decreased identical match ratio, which indicates that a homologous pair exhibits a high rate of diversification. In the case of A, the identical match ratio is "0.78".
Nishimura et al. BMC Genomics 2012 13:289 doi:10.1186/1471-2164-13-289