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

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

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7 p.

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Revanna, Kashi V.; Munro, Daniel; Gao, Alvin; Chiu, Chi-Chen; Pathak, Anil & Dong, Qunfeng August 2, 2012.

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This article is part of the collection entitled: UNT Scholarly Works and was provided by UNT College of Arts and Sciences to Digital Library, a digital repository hosted by the UNT Libraries. It has been viewed 87 times . More information about this article can be viewed below.

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

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7 p.

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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.

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  • BMC Bioinformatics, 2012, London: BioMed Central

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Publication Information

  • Publication Title: BMC Bioinformatics
  • Volume: 13
  • Issue: 190
  • Peer Reviewed: Yes

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UNT Scholarly Works

The Scholarly Works Collection is home to materials from the University of North Texas community's research, creative, and scholarly activities and serves as UNT's Open Access Repository. It brings together articles, papers, artwork, music, research data, reports, presentations, and other scholarly and creative products representing the expertise in our university community. Access to some items in this collection may be restricted.

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  • August 2, 2012

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  • Nov. 30, 2012, 9:15 a.m.

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  • July 16, 2013, 2:19 p.m.

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Revanna, Kashi V.; Munro, Daniel; Gao, Alvin; Chiu, Chi-Chen; Pathak, Anil & Dong, Qunfeng. A web-based multi-genome synteny viewer for customized data, article, August 2, 2012; [London, United Kingdom]. (digital.library.unt.edu/ark:/67531/metadc122141/: accessed May 29, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT College of Arts and Sciences.