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Bioinformatics Advance Access originally published online on February 12, 2004
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Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.

Applications Note

ParSeq: searching motifs with structural and biochemical properties

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

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

Received on October 7, 2003; accepted on December 16, 2003
Advance Access Publication February 12, 2004

Summary: Searches for variable motifs such as protein-binding sites or promoter regions are more complex than the search for casual motifs. For example, in amino acid sequences comparing motifs alone mostly proves to be insufficient to detect regions that 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 and a stepwise creation of the motif description by allowing to search on previously obtained results.

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

Contact: parseq{at}informatik.uni-tuebingen.de

* To whom correspondence should be addressed.


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