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Bioinformatics Advance Access published online on July 14, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl389
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 8, 2006
Revised July 8, 2006
Accepted July 8, 2006

Applications note

SynView: a GBrowse-compatible approach to visualizing comparative genome data

Haiming Wang 1, Yanqi Su 2, Aaron J. Mackey 3, Eileen T. Kraemer 2, and Jessica C. Kissinger 4 *

1 Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602-2606, USA
2 Department of Computer Science, University of Georgia, Athens, GA 30602-7404, USA
3 Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104-6017, USA
4 Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602-2606, USA; Department of Genetics, University of Georgia, Athens, GA 30602-7223, USA

* To whom correspondence should be addressed.
Jessica C. Kissinger, E-mail: jkissing{at}uga.edu


  Abstract

Summary: We present SynView, a simple and generic approach to dynamically visualizing multi-species comparative genome data. It is a light-weight application based on the popular and configurable web-based GBrowse framework. It can be used with a variety of databases and provides the user with a high degree of interactivity. The tool is written in Perl and runs on top of the GBrowse framework. It is in use in the PlasmoDB (http://www.PlasmoDB.org) and the CryptoDB (http://www.CrptoDB.org) projects and can be easily integrated into other cross-species comparative genome projects.

Availability: The program and instructions are freely available at http://www.ApiDB.org/apps/SynView/.

Associate Editor: Nikolaus Rajewsky
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