Island method for estimating the statistical significance of profile-profile alignment scores |
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Authors: | Aleksandar Poleksic |
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Affiliation: | (1) Department of Computer Science, University of Northern Iowa, 50614 Cedar Falls, IA, USA |
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Abstract: | Background In the last decade, a significant improvement in detecting remote similarity between protein sequences has been made by utilizing alignment profiles in place of amino-acid strings. Unfortunately, no analytical theory is available for estimating the significance of a gapped alignment of two profiles. Many experiments suggest that the distribution of local profile-profile alignment scores is of the Gumbel form. However, estimating distribution parameters by random simulations turns out to be computationally very expensive. |
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