Multiple Sequence Alignment

Abstract

The problem of simultaneously aligning a number of sequences is referred to as multiple sequence alignment. We provide a dynamic programming algorithm for multiple alignment which extends the dynamic programming algorithm for global pairwise alignment. We describe frequency based algorithms to align a sequence against a multiple alignment and to align a multiple alignment against another multiple alignment. We introduce the method of 3D profile alignment that allows to align an amino acid sequence against a tertiary protein structure. This method is useful for tertiary structure prediction. As the dynamic programming algorithm for multiple sequence alignment is very time consuming, we provide a useful approximation algorithm and discuss the heuristic method of progressive alignment.KeywordsMultiple AlignmentDynamic Programming AlgorithmAlignment AlgorithmPairwise AlignmentTriosephosphate IsomeraseThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.