| Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment | |
Abstract/OtherAbstract
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We evaluate various methods to estimate pairwise statistical significance of a pairwise local sequence alignment in terms of statistical significance accuracy and compare it with popular database search programs in terms of retrieval accuracy on a benchmark database. Results indicate that using pairwise statistical significance using standard substitution matrices is significantly better than database statistical significance reported by BLAST and PSI-BLAST, and that it is comparable and at times significantly better than SSEARCH. An application of pairwise statistical significance to empirically determine effective gap opening penalties for protein local sequence alignment using the widely used BLOSUM matrices is also presented. |
Authors
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Ankit Agrawal, Volker P. Brendel, Xiaoqiu Huang |
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Contributors
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Int. J. of Computational Biology and Drug Design |
Publication Detail
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Publisher : Inderscience Publishers Type : - Format : - |
Date Detail
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2008-12-22 |
Subject
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database statistical significance, gap opening penalty, homologs, pairwise local alignment, pairwise statistical significance, local sequence alignment, protein sequences, homology detection, bioinformatics. |
Coverage
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- |
Relation
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ISSN online: 1756-0764 ISSN print: 1756-0756 |
Source
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IJCBDD (2008), Vol 1 Issue 4, pp 347 - 367 |
Copyright Information
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Inderscience Copyright |
Other Details
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Languages : eng |
Export Citation
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