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Bioinformatics Advance Access published online on February 9, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp078
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A web-based software system for dynamic gene cluster comparison across multiple genomes

Kashi Vishwanath Revanna , Vivek Krishnakumar and Qunfeng Dong *

Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA

*To whom correspondence should be addressed. Qunfeng Dong, E-mail: dongq{at}indiana.edu


  Abstract

Summary: Investigating the conservation of gene clusters across multiple genomes has become a standard practice in the era of comparative genomics. However, all existing software and databases rely heavily on pre-computing to identify homologous genes by genome-wide comparisons. Such pre-computing strategies lack accuracy and updating the data is computationally intensive. Since most molecular biologists are often interested only in a small cluster of genes, catering to this need, we have developed a web-based software system that allows users to upload a list of genes, perform dynamic search against the genomes of their choices and interactively visualize the gene cluster conservation using a novel multi-genome browser. Our approach avoids expensive genome wide pre-computing and allows users to dynamically change the search criteria to fit their genes of interest. Our system can be customized for any genome sequences. We have applied it to both prokaryotic and eukaryotic genomes to illustrate its usability.

Availability: Our software is freely available at http://cgcv.cgb.indiana.edu/cgi-bin/index.cgi.

Contact: dongq{at}indiana.edu

Associate Editor: Prof. Dmitrij Frishman

Received on November 18, 2008; revised on February 1, 2009; accepted on February 4, 2009

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