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Increasing the accuracy of global alignment of amino acid sequences by constructing a set of alignment candidates

  • Molecular Biophysics
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Abstract

The accuracy of global Smith-Waterman alignments and Pareto-optimal alignments depending on the degree of sequence similarity (percent of coincidence, %id, and the number of removed fragments NGap) has been examined. An algorithm for constructing a set of three to six alignments has been developed of which the best alignment on the average exceeds in accuracy the best alignment that can be constructed using the Smith-Waterman algorithm. For weakly homologous sequences (%id 15, NGap 20), the increase in accuracy is on the average about 8%, with the average accuracy of the global Smith-Waterman alignments being about 38% (the accuracy was estimated on model test sets).

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Authors and Affiliations

  1. Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia

    V. V. Yakovlev & M. A. Roytberg

Authors
  1. V. V. Yakovlev
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  2. M. A. Roytberg
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Original Russian Text © V.V. Yakovlev, M.A. Roytberg, 2010, published in Biofizika, 2010, Vol. 55, No. 6, pp. 965–975.

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Yakovlev, V.V., Roytberg, M.A. Increasing the accuracy of global alignment of amino acid sequences by constructing a set of alignment candidates. BIOPHYSICS 55, 891–900 (2010). https://doi.org/10.1134/S0006350910060011

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  • DOI: https://doi.org/10.1134/S0006350910060011

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