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

BMC Bioinformatics

Software

Ezekiel Bierschank¹  Kashi V Revanna¹  Qunfeng Dong²  Chi-Chen Chiu³ 

[1] Department of Biological Sciences, University of North Texas, 76203, Denton, Texas, USA;Department of Biological Sciences, University of North Texas, 76203, Denton, Texas, USA;Department of Computer Science and Engineering, University of North Texas, 76203, Denton, Texas, USA;Department of Computer Science and Engineering, University of North Texas, 76203, Denton, Texas, USA;

关键词: Genomic Feature;    Alignment Score;    Annotation File;    Individual Genome;    Local Installation;   

DOI  :  10.1186/1471-2105-12-316

 received in 2011-04-18, accepted in 2011-08-02,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionsGSV 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, and the software is also freely available for local installations.

【 授权许可】

Unknown   
© Revanna et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.