Nucleic Acids Research, 1988, Vol. 16, No. 22 10881-10890
© 1988
MOLECULAR BIOLOGY |
Multiple sequence alignment with hierarchical clustering
Laboratoire de Génétique Cellulaire, INRA Toulouse BP 27, 31326 Castanet Tolosan, France
Received July 7, 1988. Revised October 14, 1988. Accepted October 14, 1988.
An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the process can be performed. The method is illustrated by an example : a global alignment of 39 sequences of cytochrome c.
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