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Estimation of the quality of global alignment of amino acid sequences based on evolution criterion

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Abstract

The aim of the work is to develop a common method for estimating the pairwise alignment quality versus the evolutionary distance (degree of homology) between the sequences being compared and versus the type of alignment procedure. 3D alignments or any data on 3D protein structure are not used in the study. Based on the accepted protein sequences evolution model, it is possible to estimate the capability of the concrete alignment algorithm to recover the genuine alignment. In this study a classical Needleman and Wunsch global alignment algorithm has been tested on a set of sequences from the Prefab database. Accuracy and confidence of a global alignment procedure were calculated as dependent on the shares of insertions/deletions and mutations.

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Authors and Affiliations

  1. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia

    V. O. Polyanovskii & V. G. Tumanyan

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  1. V. O. Polyanovskii
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  2. V. G. Tumanyan
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Correspondence to V. O. Polyanovskii.

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Original Russian Text © V.O. Polyanovskii, V.G. Tumanyan, 2013, published in Biofizika, 2013, Vol. 58, No. 2, pp. 197–202.

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Polyanovskii, V.O., Tumanyan, V.G. Estimation of the quality of global alignment of amino acid sequences based on evolution criterion. BIOPHYSICS 58, 137–141 (2013). https://doi.org/10.1134/S0006350913020140

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  • DOI: https://doi.org/10.1134/S0006350913020140

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