Format

Send to

Choose Destination
See comment in PubMed Commons below
Nucleic Acids Res. 2004 May 20;32(9):2838-43. Print 2004.

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

Author information

1
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.

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 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.

PMID:
15155852
PMCID:
PMC419611
DOI:
10.1093/nar/gkh610
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center