Pairwise statistical significance of local sequence alignment using substitution matrices with sequence-pair-specific distance

Ankit Agrawal*, Xiaoqiu Huang

*Corresponding author for this work

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

10 Scopus citations

Abstract

Pairwise sequence alignment forms the basis of numerous other applications in bioinformatics. The quality of an alignment is gauged by statistical significance rather than by alignment score alone. Therefore, accurate 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, and also provides quicker individual pairwise estimates of statistical significance without having to perform time-consuming database search. Under an evolutionary model, a substitution matrix can be derived using a rate matrix and a fixed distance. Although the commonly used substitution matrices like BLOSUM62, etc. were not originally derived from a rate matrix under an evolutionary model, the corresponding rate matrices can be back calculated. Many researchers have derived different rate matrices using different methods and data. In this paper, we show that pairwise statistical significance using rate matrices with sequence-pair-specific distance performs significantly better compared to using a fixed distance. Pairwise statistical significance using sequence-pair-specific distanced substitution matrices also outperforms database statistical significance reported by BLAST.

Original languageEnglish (US)
Title of host publicationProceedings - 11th International Conference on Information Technology, ICIT 2008
Pages94-99
Number of pages6
DOIs
StatePublished - Dec 1 2008
Event11th International Conference on Information Technology, ICIT 2008 - Bhubaneswar, India
Duration: Dec 17 2008Dec 20 2008

Publication series

NameProceedings - 11th International Conference on Information Technology, ICIT 2008

Other

Other11th International Conference on Information Technology, ICIT 2008
CountryIndia
CityBhubaneswar
Period12/17/0812/20/08

ASJC Scopus subject areas

  • Computer Science Applications
  • Information Systems
  • Software

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  • Cite this

    Agrawal, A., & Huang, X. (2008). Pairwise statistical significance of local sequence alignment using substitution matrices with sequence-pair-specific distance. In Proceedings - 11th International Conference on Information Technology, ICIT 2008 (pp. 94-99). [4731306] (Proceedings - 11th International Conference on Information Technology, ICIT 2008). https://doi.org/10.1109/ICIT.2008.63