FAVAT scoring example For the first position of the target sequence, four V-scores were calculated for L-L-Y, L-LY, L-K-Y and L-K-Y, respectively. The T-score at each position is the sum of four V-scores, and the T-score (total score) for the first position of the target sequence is 4. After the normalization function, the final T-score is 52. When any gap existed at the position in one of three groups such as column 11, the T-score for this position is zero.
Hung et al. BMC Genomics 2010 11(Suppl 3):S14 doi:10.1186/1471-2164-11-S3-S14