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Bioinformatics Vol. 19 no. 6 2003
Pages 784-785
© 2003 Oxford University Press

Applications Note

EPPS: mining the COG database by an extended phylogenetic patterns search

Klaus Reichard 1 and Michael Kaufmann 2,*

1 Institute of Mathematics, AG Statistics
2 Institute of Neurobiochemistry, AG Proteinchemistry, University of Witten/Herdecke, Stockumer Str. 10, 58448 Witten, Germany

Received on July 7, 2002 ; revised on November 8, 2002 ; accepted on December 14, 2002

Summary: EPPS runs under Microsoft Windows. It is an extended version of the phylogenetic patterns search (PPS). The output condition of PPS is the exact match of a user defined phylogenetic pattern with the pattern represented by the respective cluster of orthologous groups (COG). In contrast, the software described here is less restrictive. The user may define the accuracy of the search by the number of genomes that are allowed not to match the predefined phylogenetic pattern. Thus, EPPS has the advantage to detect COGs even if organisms defined to be included are not or organisms defined to be excluded are present in the output COGs.

Availability: EPPS is free and both windows executable and source code are available at http://www.uni-wh.de/de/nawi/institut/protein/epps.html

Contact: mika{at}uni-wh.de

* To whom correspondence should be addressed.


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