Research on multiple alignments for alternative splicing

A heuristic algorithm for multiple alignment was developed to more effectively study alternative splicing patterns of eukaryotic genes. The segment-to-segment alignment is guided by a guide-tree. The time for constructing the guide-tree is reduced remarkably by adopting a similarity estimation model which estimates the similarities between sequences from the total number of hits. The segment-to-segment alignment eliminates the problem introduced by the gap which exits in traditional alignments so that alternative splicing patterns are revealed more precisely. The new method for constructing the guide-tree combined with the basic local alignment search tool increases the algorithm speed compared with other multiple alignment algorithms. This algorithm is a new way to study alternative splicing.