Affordable Access

Access to the full text

H-Tuple Approach to Evaluate Statistical Significance of Biological Sequence Comparison with Gaps

Authors
  • Fayyaz movaghar, Afshin
  • Mercier, Sabine
  • Ferré, Louis
Type
Published Article
Journal
Statistical Applications in Genetics and Molecular Biology
Publisher
Walter de Gruyter GmbH
Publication Date
Aug 25, 2007
Volume
6
Issue
1
Identifiers
DOI: 10.2202/1544-6115.1272
Source
De Gruyter
Keywords
License
Yellow

Abstract

We propose an approximate distribution for the gapped local score of a two sequence comparison. Our method stands on combining an adapted scoring scheme that includes the gaps and an approximate distribution of the ungapped local score of two independent sequences of i.i.d. random variables. The new scoring scheme is defined on h-tuples of the sequences, using the gapped global score. The influence of h and the accuracy of the p-value are numerically studied and compared with obtained p-value of BLAST. The numerical experiments emphasize that our approximate p-values outperform the BLAST ones, particularly for both simulated and real short sequences.

Report this publication

Statistics

Seen <100 times