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

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

doi:10.1007/11758525_89

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

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

Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	Computational Science - ICCS 2006
Subtitle of host publication	6th International Conference, Proceedings
Publisher	Springer Verlag
Pages	654-661
Number of pages	8
ISBN (Print)	3540343814, 9783540343813
DOIs	https://doi.org/10.1007/11758525_89
State	Published - 2006
Event	ICCS 2006: 6th International Conference on Computational Science - Reading, United Kingdom Duration: May 28 2006 → May 31 2006

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	3992 LNCS - II
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	ICCS 2006: 6th International Conference on Computational Science
Country/Territory	United Kingdom
City	Reading
Period	5/28/06 → 5/31/06

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/11758525_89

Cite this

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

COMBAT: Search rapidly for highly similar protein-coding sequences using bipartite graph matching. / Sun, Bing; Schwartz, Jacob T.; Gill, Ofer H. et al.
Computational Science - ICCS 2006: 6th International Conference, Proceedings. Springer Verlag, 2006. p. 654-661 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3992 LNCS - II).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Sun, B, Schwartz, JT, Gill, OH & 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. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3992 LNCS - II, Springer Verlag, pp. 654-661, ICCS 2006: 6th International Conference on Computational Science, Reading, United Kingdom, 5/28/06. https://doi.org/10.1007/11758525_89

Sun B, Schwartz JT, Gill OH, Mishra B. COMBAT: Search rapidly for highly similar protein-coding sequences using bipartite graph matching. In Computational Science - ICCS 2006: 6th International Conference, Proceedings. Springer Verlag. 2006. p. 654-661. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/11758525_89

Sun, Bing ; Schwartz, Jacob T. ; Gill, Ofer H. et al. / COMBAT : Search rapidly for highly similar protein-coding sequences using bipartite graph matching. Computational Science - ICCS 2006: 6th International Conference, Proceedings. Springer Verlag, 2006. pp. 654-661 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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

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