Multiple sequence alignment using anchor points through generalized dynamic programming
نویسندگان
چکیده
A generalization of the dynamic programming algorithm applied to the multiple alignment of protein sequences is proposed. The algorithm has two main procedures: (i) local correspondences between sequences hereafter called anchor points are selected according to a criterion that combines local and global simlilarity values, (ii) the alignment is constructed recursively by choosing and linking together the optimal anchor points. This multiple sequence alignment algorithm achieves a good compromise between the O(L N ) complexity of the exhaustive dynamic programming approach applied to N sequences of length L and the poor quality of the alignments obtained with methods based on a hierarchical clustering of the sequences.
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