A technique of genetic algorithm and sequence synthesis for multiple molecular sequence alignment

The currently used techniques for multiple sequence alignment are characterized by great computational complexity, which prevents the techniques from wider use. The research reported in the paper is aimed at developing a new technique for efficient multiple sequence alignment. The new technique consists of a genetic algorithm and a sequence synthesis method. The genetic algorithm identifies matches and the sequence synthesis method handles mismatches. Genetic algorithms are stochastic approaches for efficient and robust search. By converting biomolecular sequence alignment into a problem of searching for near-optimal points in a "pre-alignment space", a genetic algorithm can be used to find good alignments very efficiently. Experiments on real data sets have shown that the average computing time of this technique may be two or three orders lower than an technique based on pairwise dynamic programming, while the alignment qualities are very similar.