Score setting and scoring example (a) Substitution matrix for BLOSUM62. In this study, the BLOSUM 62 substitution matrix was used to obtain V-scores for the voting algorithm. (b) Example of FAVAT scoring. When three-profile alignment was performed in the target sequence, the voting scores for A proteins and ~A proteins corresponded with the BLOSUM62 substitution matrix. For example, residues for target sequence, an A protein and a ~A protein were A, H and L, respectively. The V-score is -2 (A to H in BLOSUM62) - (-1) (A to L in BLOSUM62) = -1.
Hung et al. BMC Genomics 2010 11(Suppl 3):S14 doi:10.1186/1471-2164-11-S3-S14