Optimal sequence alignment using affine gap costs (original) (raw)

Abstract

When comparing two biological sequences, it is often desirable for a gap to be assigned a cost not directly proportional to its length. If affine gap costs are employed, in other words if opening a gap costs_v_ and each null in the gap costs_u_, the algorithm of Gotoh (1982,J. molec. Biol. 162, 705) finds the minimum cost of aligning two sequences in order_MN_ steps. Gotoh's algorithm attempts to find only one from among possibly many optimal (minimum-cost) alignments, but does not always succeed. This paper provides an example for which this part of Gotoh's algorithm fails and describes an algorithm that finds all and only the optimal alignments. This modification of Gotoh's algorithm still requires order_MN_ steps. A more precise form of path graph than previously used is needed to represent accurately all optimal alignments for affine gap costs.

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Authors and Affiliations

1. The Rockefeller University, 10021, New York, NY, U.S.A.
   Stephen F. Altschul & Bruce W. Erickson
2. Department of Applied Mathematics, Massachusetts Institute of Technology, 02139, Cambridge, MA, U.S.A.
   Stephen F. Altschul

Authors

1. Stephen F. Altschul
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2. Bruce W. Erickson
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Altschul, S.F., Erickson, B.W. Optimal sequence alignment using affine gap costs.Bltn Mathcal Biology 48, 603–616 (1986). https://doi.org/10.1007/BF02462326

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• Received: 17 February 1986
• Issue Date: September 1986
• DOI: https://doi.org/10.1007/BF02462326

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