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Article

Empirical determination of effective gap penalties for sequence comparison.

Bioinformatics (Oxford, England) - 1 Nov 2002

Reese J T, Pearson W R

Abstract excerpt

MOTIVATION: No general theory guides the selection of gap penalties for local sequence alignment. We empirically determined the most effective gap penalties for protein sequence similarity searches with substitution matrices over a range of target evolutionary distances from 20 to 200 Point Accepted Mutations (PAMs). RESULTS: We embedded real and simulated homologs of protein sequences into a database and...

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Source

Identifiers

PMID: 12424122
DOI: 10.1093/bioinformatics/18.11.1500

Genes

PAM

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Source receipt: pubmed, retrieved 7 Sept 2026.

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