COMBAT: Search rapidly for highly similar protein-coding sequences using bipartite graph matching

Bing Sun, Jacob T. Schwartz, Ofer H. Gill, Bud Mishra

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

Abstract

Comparing vertebrate genomes requires efficient cross-species sequence alignment programs. We describe COMBAT, a new mer-based method which can search rapidly for highly similar translated genomic sequences, with the stable-marriage algorithm with incomplete lists (SMI) as a filter scheme. We apply the COMBAT program to the comparative analysis of the human with the most recent bovine genome assemblies, and 84%-95% of the homologous blocks identified by this program are confirmed by BLASTZ.

Original languageEnglish (US)
Title of host publicationComputational Science - ICCS 2006
Subtitle of host publication6th International Conference, Proceedings
PublisherSpringer Verlag
Pages654-661
Number of pages8
ISBN (Print)3540343814, 9783540343813
DOIs
StatePublished - 2006
EventICCS 2006: 6th International Conference on Computational Science - Reading, United Kingdom
Duration: May 28 2006May 31 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3992 LNCS - II
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

OtherICCS 2006: 6th International Conference on Computational Science
CountryUnited Kingdom
CityReading
Period5/28/065/31/06

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Sun, B., Schwartz, J. T., Gill, O. H., & Mishra, B. (2006). COMBAT: Search rapidly for highly similar protein-coding sequences using bipartite graph matching. In Computational Science - ICCS 2006: 6th International Conference, Proceedings (pp. 654-661). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3992 LNCS - II). Springer Verlag. https://doi.org/10.1007/11758525_89