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Bioinformatics Advance Access published online on February 19, 2007
Bioinformatics, 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

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

*to whom correspondence should be addressed. Jan Krumsiek, E-mail: krumsiek{at}in.tum.de


  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 O(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

Associate Editor: Martin Bishop

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

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[Abstract] [Full Text] [PDF]


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