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Open Access Highly Accessed Software

GSV: a web-based genome synteny viewer for customized data

Kashi V Revanna1, Chi-Chen Chiu2, Ezekiel Bierschank1 and Qunfeng Dong12*

Author Affiliations

1 Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA

2 Department of Computer Science and Engineering, University of North Texas, Denton, Texas 76203, USA

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BMC Bioinformatics 2011, 12:316  doi:10.1186/1471-2105-12-316

Published: 2 August 2011

Abstract

Background

The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis.

Results

We have developed the web-based Genome Synteny Viewer (GSV) that allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation.

Conclusions

GSV provides a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. A web server hosting GSV is provided at http://cas-bioinfo.cas.unt.edu/gsv webcite, and the software is also freely available for local installations.