MASCOT - MULTIPLE ALIGNMENT SYSTEM FOR PROTEIN SEQUENCES BASED ON 3-WAY DYNAMIC-PROGRAMMING

A multiple alignment methodology that can produce high-quality alignme nt is extremely important for predicting the structure of unknown prot eins. Nearly all the methodologies developed so far have employed two- way alignment only. Although these methods are fast, the alignments th ey produce lose reliability as the similarity of sequences reduces. We developed the MASCOT multiple alignment system. MASCOT can sustain th e reliability of alignment even when the similarity of sequences is lo w. MASCOT achieves high-quality alignment by employing three-way align ment in addition to two-way alignment. The resultant alignments are re fined by simulated annealing to higher quality. We also use a cluster analysis of sequences to produce highly reliable alignments.