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An online conserved SSR discovery through cross-species comparison

Authors Tun-Wen Pai, Chien-Ming Chen, Meng-Chang Hsiao, Ronshan Cheng, Wen-Shyong Tzou, Chin-Hua Hu

Published 8 February 2009 Volume 2009:2 Pages 23—35

DOI https://doi.org/10.2147/AABC.S4744

Review by Single-blind

Peer reviewer comments 4

Tun-Wen Pai1, Chien-Ming Chen1, Meng-Chang Hsiao1, Ronshan Cheng2, Wen-Shyong Tzou3, Chin-Hua Hu3

1Department of Computer Science and Engineering; 2Department of Aquaculture, 3Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan, Republic of China

Abstract: Simple sequence repeats (SSRs) play important roles in gene regulation and genome evolution. Although there exist several online resources for SSR mining, most of them only extract general SSR patterns without providing functional information. Here, an online search tool, CG-SSR (Comparative Genomics SSR discovery), has been developed for discovering potential functional SSRs from vertebrate genomes through cross-species comparison. In addition to revealing SSR candidates in conserved regions among various species, it also combines accurate coordinate and functional genomics information. CG-SSR is the first comprehensive and efficient online tool for conserved SSR discovery.

Keywords: microsatellites, genome, comparative genomics, functional SSR, gene ontology, conserved region

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