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Nucleic Acids Research, 1984, Vol. 12, No. 1Part2 447-455
© 1984

MINICOMPUTERS

A fast homology program for aligning biological sequences

Philip Taylor

Institute of Virology, University of Glasgow Church Street, Glasgow G1l 5JR, UK

Received June 7, 1983. The algorithm of Gotoh1 computes in two passes of MN steps the alignment of a pair of sequences of lengths M and N, subject to a constraint on the form of the gap weighting function. This compares with the previous algorithm of Waterman et al.2 which runs in M2n steps. Gotoh1 also gave a method using two passes of (L+2)MN steps in the case where gap weights remain constant for gaps of length greater than L.

Here we describe a procedure for computing the alignment (evolutionary distance and optimal path) in a single pass of MN steps for both cases.


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