OrthoCluster: a new tool for mining synteny blocks and applications in comparative genomics

By comparing genomes among both closely and distally related species, comparative genomics analysis characterizes structures and functions of different genomes in both conserved and divergent regions. Synteny blocks, which are conserved blocks of genes on chromosomes of related species, play important roles in comparative genomics analysis. Although a few tools have been designed to identify synteny blocks, most of them cannot handle some challenging application requirements, particularly the strandedness of genes, gene inversions, gene duplications, and comparison of more than two genomes. We developed a data mining tool, OrthoCluster, which can handle all those challenges. It is publicly available at http://genome.sfu.ca/projects/orthocluster. OrthoCluster takes the annotated gene sets of candidate genomes and pairwise orthologous relationships as input and efficiently identifies the complete set of synteny blocks. In addition, OrthoCluster identifies four types of genome rearrangem...

• Type: Conference
• Year: 2008
• Where: EDBT
• Authors: Xinghuo Zeng, Matthew J. Nesbitt, Jian Pei, Ke Wang, Ismael A. Vergara, Nansheng Chen
• Keywords: Annotated Gene Sets, Candidate Genomes, Comparative Genomics Analysis, Database, EDBT 2008