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

Description:

This article discusses a web-based multi-genome synteny viewer for customized data.

Creator(s):
Creation Date: August 2, 2012
Partner(s):
UNT College of Arts and Sciences
Collection(s):
UNT Scholarly Works
Usage:
Total Uses: 36
Past 30 days: 1
Yesterday: 1
Creator (Author):
Revanna, Kashi V.

University of North Texas

Creator (Author):
Munro, Daniel

University of North Texas

Creator (Author):
Gao, Alvin

University of North Texas

Creator (Author):
Chiu, Chi-Chen

University of North Texas

Creator (Author):
Pathak, Anil

University of North Texas

Creator (Author):
Dong, Qunfeng

University of North Texas

Publisher Info:
Publisher Name: BioMed Central
Place of Publication: [London, United Kingdom]
Date(s):
  • Creation: August 2, 2012
Description:

This article discusses a web-based multi-genome synteny viewer for customized data.

Degree:
Department: Biological Sciences
Note:

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, the authors 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: The authors 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 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 functionality of GSV. A web server hosting mGSV is provided at http://cas-bioinfo.cas.unt.edu/mgsv.

Physical Description:

7 p.

Language(s):
Subject(s):
Keyword(s): genomes | centralized web resources | multi-Genome Synteny Viewer | mGSV
Source: BMC Bioinformatics, 2012, London: BioMed Central
Partner:
UNT College of Arts and Sciences
Collection:
UNT Scholarly Works
Identifier:
  • DOI: 10.1186/1471-2105-13-190
  • ARK: ark:/67531/metadc122141
Resource Type: Article
Format: Text
Rights:
Access: Public
Citation:
Publication Title: BMC Bioinformatics
Volume: 13
Issue: 190
Peer Reviewed: Yes