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Open Access Highly Accessed Software

A web-based multi-genome synteny viewer for customized data

Kashi V Revanna1, Daniel Munro1, Alvin Gao2, Chi-Chen Chiu3, Anil Pathak3 and Qunfeng Dong13*

Author affiliations

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

2 The Texas Academy of Mathematics and Science, University of North Texas, Denton, Texas, 76203, USA

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

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Citation and License

BMC Bioinformatics 2012, 13:190  doi:10.1186/1471-2105-13-190

Published: 2 August 2012

Abstract

Background

Web-based synteny visualization tools are important for sharing data and revealing patterns of complicated genome conservation and rearrangements. Such tools should allow biologists to upload genomic data for their own analysis. This requirement is critical because individual biologists are generating large amounts of genomic sequences that quickly overwhelm any centralized web resources to collect and display all those data. Recently, we published a web-based synteny viewer, GSV, which was designed to satisfy the above requirement. However, GSV can only compare two genomes at a given time. Extending the functionality of GSV to visualize multiple genomes is important to meet the increasing demand of the research community.

Results

We have developed a multi-Genome Synteny Viewer (mGSV). Similar to GSV, mGSV is a web-based tool that allows users to upload their own genomic data files for visualization. Multiple genomes can be presented in a single integrated view with an enhanced user interface. Users can navigate through all the selected genomes in either pairwise or multiple viewing mode to examine conserved genomic regions as well as the accompanying genome annotations. Besides serving users who manually interact with the web server, mGSV also provides Web Services for machine-to-machine communication to accept data sent by other remote resources. The entire mGSV package can also be downloaded for easy local installation.

Conclusions

mGSV significantly enhances the original functionalities of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv webcite.