Comparison of alignment accuracy on the basis of sequence similarity. Conserved motifs are identified for superfamilies like, Cytochromes (code: 02.01.050), ACP-like (02.01.060), C2 domain (Calcium/lipid-binding domain, CaLB) (code: 02.02.027), ISP domain (code: 02.02.058), Phosphatidylinositol-specific phospholipase C (PI-PLC) (code: 02.03.018), Esterase/acetylhydrolase (02.03.054), Chromo domain-like (code: 02.04.010) and BPTI-like (02.07.023). These motifs are utilized to realign the sequences by FMALIGN. Alignments are scored using sequence similarity scores based on a 20x20 substitution matrix. FMALIGN derived alignments are compared against CLUSTALX  and sequence-structure alignment, COMPARER .
Chakrabarti et al. BMC Bioinformatics 2004 5:167 doi:10.1186/1471-2105-5-167