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Published online 20 May 2004

Nucleic Acids Research, 2004, Vol. 32, No. 9 2838-2843

Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function

Nalin C. W. Goonesekere and Byungkook Lee*

Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 5120, 37 Convent Drive MSC 4264, Bethesda, MD 20892-4264, USA

*To whom correspondence should be addressed. Tel: +1 301 496 6580; Fax: +1 301 480 4654; Email: bk{at}nih.gov

Received February 3, 2004; Revised and Accepted April 23, 2004

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 x 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.


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