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Bioinformatics Advance Access originally published online on February 19, 2007
Bioinformatics 2007 23(8):1026-1028; doi:10.1093/bioinformatics/btm039
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Gepard: a rapid and sensitive tool for creating dotplots on genome scale

Jan Krumsiek 1,*, Roland Arnold 1 and Thomas Rattei 2

1Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstädter Landstraße 1, 85764 Neuherberg and 2Technische Universität München, Department of Genome Oriented Bioinformatics, Am Forum 1, 85354 Freising, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: Gepard provides a user-friendly, interactive application for the quick creation of dotplots. It utilizes suffix arrays to reduce the time complexity of dotplot calculation to {Theta}(m*log n). A client–server mode, which is a novel feature for dotplot creation software, allows the user to calculate dotplots and color them by functional annotation without any prior downloading of sequence or annotation data.

Availability: Both source codes and executable binaries are available at http://mips.gsf.de/services/analysis/gepard

Contact: krumsiek{at}in.tum.de

Associate Editor: Martin Bishop

Received on October 13, 2006; revised on January 30, 2007; accepted on January 31, 2007

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