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Bioinformatics Advance Access published online on February 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth083
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received October 7, 2003
Revised December 16, 2003
Accepted December 16, 2003

Applications note

ParSeq: searching motifs with structural and biochemical properties

M. Schmollinger 1*, I. Fischer 1, C. Nerz 1, S. Pinkenburg 1, F. Götz 1, M. Kaufmann 1, K.-J. Lange 1, R. Reuter 1, W. Rosenstiel 1, A. Zell 1

1 Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany

* To whom correspondence should be addressed. E-mail: parseq{at}informatik.uni-tuebingen.de.


  Abstract

Summary: Searches for variable motifs, like protein binding sites or promotor regions are more complex than the search for casual motifs, e. g. on amino acid sequences comparing motifs alone mostly proves to be insufficient to detect regions, which represent proteins with a special function, because the function depends on biochemical properties of individual amino acids (such as polarity or hydrophobicity). Pure string matching programs are not able to find these motifs, hence, we developed ParSeq, a program that combines the search for motifs with certain structural properties, the verification of biochemical properties, an approximate search mechanism, a stepwise creation of the motif description by allowing to search on previously obtained results.

Availability: http://www-pr.informatik.uni-tuebingen.de/parseq


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