Faculty Publications

Frequency of Gaps Observed in a Structurally Aligned Protein Pair Database Suggest a Simple Gap Penalty Function

Document Type

Article

Journal/Book/Conference Title

Nucleic Acids Research

Volume

32

Issue

9

First Page

2838

Last Page

2843

Abstract

Gap penalty is an important component of the scoring scheme that is needed when searching for homologous proteins and for accurate alignment of protein sequences. Most homology search and sequence alignment algorithms employ a heuristic 'affine gap penalty' scheme q + r × n, in which q is the penalty for opening a gap, r the penalty for extending it and n the gap length. In order to devise a more rational scoring scheme, we examined the pattern of gaps that occur in a database of structurally aligned protein domain pairs. We find that the logarithm of the frequency of gaps varies linearly with the length of the gap, but with a break at a gap of length 3, and is well approximated by two linear regression lines with R2 values of 1.0 and 0.99. The bilinear behavior is retained when gaps are categorized by secondary structures of the two residues flanking the gap. Similar results were obtained when another, totally independent, structurally aligned protein pair database was used. These results suggest a modification of the affine gap penalty function. © Oxford University Press 2004; all rights reserved.

Department

Department of Chemistry and Biochemistry

Original Publication Date

7-20-2004

DOI of published version

10.1093/nar/gkh610

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