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Bioinformatics Advance Access published online on April 29, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn213
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

jSquid: a Java applet for graphical on-line network exploration

Martin Klammer 1,2,{dagger}, Sanjit Roopra 1,2,{dagger} and Erik L. L. Sonnhammer 1,*

1Stockholm Bioinformatics Centre, Stockholm University, 10691 Stockholm, Sweden
2Department of Bioinformatics, Upper Austrian University of Applied Sciences, 4232 Hagenberg, Austria

*To whom correspondence should be addressed. Prof. Erik L. L. Sonnhammer, E-mail: erik.sonnhammer{at}sbc.su.se


  Abstract

Summary: jSquid is a graph visualization tool for exploring graphs from protein-protein interaction or functional coupling networks. The tool was designed for the FunCoup web site, but can be used for any similar network exploring purpose. The program offers various visualization and graph manipulation techniques to increase the utility for the user.

Availability: jSquid is available for direct usage and download at http://jSquid.sbc.su.se including source code under the GPLv3 license, and input examples. It requires Java version 5 or higher to run properly.

Contact: erik.sonnhammer{at}sbc.su.se

Supplementary Information: available at Bioinformatics online

Associate Editor: Prof. Thomas Lengauer

{dagger}These authors contributed equally to this work.

Received on February 12, 2008; revised on April 28, 2008; accepted on April 28, 2008

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