COMBAT: Search Rapidly for Highly Similar Protein-Coding Sequences Using Bipartite Graph Matching

  • Bing Sun
  • Jacob T. Schwartz
  • Ofer H. Gill
  • Bud Mishra
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3992)


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.


Stable Match Preference List Stable Marriage Stable Marriage Problem Match Partner 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Bing Sun
    • 1
  • Jacob T. Schwartz
    • 1
  • Ofer H. Gill
    • 1
  • Bud Mishra
    • 1
  1. 1.Courant Institute of Mathematical SciencesNew York UniversityNew YorkUSA

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