Approximate p-values for local sequence alignments: numerical studies.

J D Storey; D Siegmund

doi:10.1089/106652701753216530

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PubMed · 11694182

Approximate p-values for local sequence alignments: numerical studies.

J D Storey·D Siegmund

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Abstract

Siegmund and Yakir (2000) have given an approximate p-value when two independent, identically distributed sequences from a finite alphabet are optimally aligned based on a scoring system that rewards similarities according to a general scoring matrix and penalizes gaps (insertions and deletions). The approximation involves an infinite sequence of difficult-to-compute parameters. In this paper, it is shown by numerical studies that these reduce to essentially two numerically distinct parameters, which can be computed as one-dimensional numerical integrals. For an arbitrary scoring matrix and affine gap penalty, this modified approximation is easily evaluated. Comparison with published numerical results show that it is reasonably accurate.

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Models, Molecular Sequence Alignment Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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J D Storey, D Siegmund. 2001. Approximate p-values for local sequence alignments: numerical studies.. https://doi.org/10.1089/106652701753216530

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