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Bioinformatics. 2009 Apr 1;25(7):956-7. doi: 10.1093/bioinformatics/btp078. Epub 2009 Feb 9.

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

Author information

1
Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA.

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-computation 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.

PMID:
19208612
DOI:
10.1093/bioinformatics/btp078
[Indexed for MEDLINE]

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