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Algorithms for computing evolutionary similarity measures with length independent gap penalties (1984)

Fredman, M. L.

Springer

Bulletin of mathematical biology 46 (1984), S. 553-566

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ISSN: 1522-9602

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Mathematics

Notes: Abstract We give algorithms for computing the extent of similarity between two or three sequences of letters. The similarity measures we consider include a penalty for inserting gaps within the sequence in order to enhance similarity. The magnitude of the penalty for gaps is assumed to be independent of their size in order to accommodate certain biological applications. Our algorithm for three sequence comparisons, which is based on solving a system of recursive equations, improves upon the efficiency of existing methods. Although the system of recursive equations utilized by the algorithm is quite complicated as it stands, it has none the less been simplified by appeal to combinatorial considerations.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF02459503

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