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Consistency of optimal sequence alignments

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Abstract

Pairwise optimal alignments between three or more sequences are not necessarily consistent as a whole, but consistent and inconsistent residues are usually distributed in clusters. An efficient method has been developed for locating consistent regions when each pairwise alignment is given in the form of a “skeletal representation” (Bull. math. Biol. 52, 359–373). This method is further extended so that the combination of pairwise alignments that gives the greatest consistency is found when possibly many alignments are equally optimal for each pairwise comparison. A method for acceleration of simultaneous multiple sequence alignment is proposed in which consistent regions serve as “anchor points” limiting application of direct multi-way alignment to the rest of “inconsistent” regions.

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Author notes

  1. Osamu Gotoh

    Present address: Department of Biochemistry, Saitama Cancer Center Research Institute, Ina-machi, 362, Saitama, Japan

Authors and Affiliations

  1. Graduate School of Biomedical Sciences, Genetics Centers, The University of Texas, Health Science Center at Houston, P.O. Box 20334, 77225, Houston, TX, USA

    Osamu Gotoh

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  1. Osamu Gotoh
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Dedicated to Prof. Akiyoshi Wada on the occasion of his 60th birthday.

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Gotoh, O. Consistency of optimal sequence alignments. Bltn Mathcal Biology 52, 509–525 (1990). https://doi.org/10.1007/BF02462264

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  • DOI: https://doi.org/10.1007/BF02462264

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