Abstract
A generalization of the dynamic programming algorithm applied to the multiple align-ment of protein sequences is proposed. The algorithm has two main procedures:(i) local correspondences between sequences-hereafter called anchor points-are selected accord-ing 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 (LN) 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 hierar-chical clustering of the sequences.
