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

Description:

Article discussing the genome synteny viewer (GSV), a web-based viewer providing a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser.

Creator(s):
Creation Date: 2011  
Partner(s):
UNT College of Arts and Sciences
Collection(s):
UNT Scholarly Works
Usage:
Total Uses: 77
Past 30 days: 13
Yesterday: 1
Creator (Author):
Revanna, Kashi V.

University of North Texas

Creator (Author):
Chiu, Chi-Chen

University of North Texas

Creator (Author):
Bierschank, Ezekiel

University of North Texas

Creator (Author):
Dong, Qunfeng

University of North Texas

Publisher Info:
Publisher Name: BioMed Central Ltd.
Place of Publication: [London, United Kingdom]
Date(s):
  • Creation: 2011
Description:

Article discussing the genome synteny viewer (GSV), a web-based viewer providing a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser.

Degree:
Department: Biological Sciences
Note:

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: The authors 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, and the software is also freely available for local installations.

Physical Description:

4 p.

Language(s):
Subject(s):
Keyword(s): genomics | genome synteny viewers | GSV
Source: BMC Informatics, 2011, London: BioMed Central Ltd.
Partner:
UNT College of Arts and Sciences
Collection:
UNT Scholarly Works
Identifier:
  • DOI: 10.1186/1471-2105-12-316
  • ARK: ark:/67531/metadc77111
Resource Type: Article
Format: Text
Rights:
Access: Public
Citation:
Publication Title: BMC Bioinformatics
Volume: 12
Issue: 316
Peer Reviewed: Yes