Conservative, non-conservative and average pairwise statistical significance of local sequence alignment

Ankit Agrawal*, Xiaoqiu Huang

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations

Abstract

Estimation of statistical significance of a pairwise alignment is an important problem in sequence comparison. Recently, it was shown that pairwise statistical significance does better in practice than database statistical significance in terms of retrieval accuracy of homologs. In this paper, we introduce the concept of conservative, non-conservative, and average pairwise statistical significance which can be easily derived from original pairwise statistical significance estimates and use more information specific to the sequence pair under consideration using multiple shuffle spaces. Experimental results for homology detection reveal that the proposed measures give at least comparable or significantly better retrieval accuracy than original pairwise statistical significance and database statistical significance reported by BLAST, PSI-BLAST, and SSEARCH. The use of the proposed measures is further shown to be extremely useful when using sequence-specific substitution matrices.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages433-436
Number of pages4
DOIs
StatePublished - Dec 1 2008
Event2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States
Duration: Nov 3 2008Nov 5 2008

Publication series

NameProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Other

Other2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
CountryUnited States
CityPhiladelphia, PA
Period11/3/0811/5/08

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

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