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Approximate statistics of gapped alignments.

Mott, R; Tribe, R; (1999) Approximate statistics of gapped alignments. J Comput Biol , 6 (1) pp. 91-112. 10.1089/cmb.1999.6.91.

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Abstract

A heuristic approximation to the score distribution of gapped alignments in the logarithmic domain is presented. The method applies to comparisons between random, unrelated protein sequences, using standard score matrices and arbitrary gap penalties. It is shown that gapped alignment behavior is essentially governed by a single parameter, alpha, depending on the penalty scheme and sequence composition. This treatment also predicts the position of the transition point between logarithmic and linear behavior. The approximation is tested by simulation and shown to be accurate over a range of commonly used substitution matrices and gap-penalties.

Type: Article
Title: Approximate statistics of gapped alignments.
Location: United States
DOI: 10.1089/cmb.1999.6.91
Keywords: Amino Acid Sequence, Computational Biology, Likelihood Functions, Models, Statistical, Probability, Proteins, Regression Analysis, Sequence Alignment
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: http://discovery.ucl.ac.uk/id/eprint/1487645
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