Accelerated method for comparing amino acid sequences with allowance for possible gaps. Plotting optimum correspondence paths.

V I Pozdnyakov; Pankov YuA

doi:10.1111/j.1399-3011.1981.tb01994.x

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Accelerated method for comparing amino acid sequences with allowance for possible gaps. Plotting optimum correspondence paths.

V I Pozdnyakov·Pankov YuA

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Abstract

An accelerated method is suggested which enables an effective comparison to be made of amino acid (nucleotide) sequences of great length with due regard to a large number of possible gaps. The method consists in limiting the area of complete similarity charts, calculated in accordance with the algorithm suggested by Sankoff (1972), by a certain specially selected diagonal band. The application of the Monte-Carlo method permits a statistical evaluation to be made of the certainty of the similarity of the compared sequences and to choose on such a "comparison band", an optimum "correspondence path" which can readily be transformed into sequence alignment. Using this approach, prolactin and somatotropin families of sequences were found to be homologous at a high level of significance and their optimum alignment with two gaps has been suggested. In contrast, two regions of assumed partial gene duplication in beta-galactosidase sequence, suggested by Hood et al. (1978), were found not to be statistically significantly similar.

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Amino Acid Sequence Growth Hormone Methods Prolactin beta-Galactosidase Comparative Study Journal Article

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V I Pozdnyakov, Pankov YuA. 1981. Accelerated method for comparing amino acid sequences with allowance for possible gaps. Plotting optimum correspondence paths.. https://doi.org/10.1111/j.1399-3011.1981.tb01994.x

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