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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.

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