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Bioinformatics Vol. 18 no. 8 2002
Pages 1091-1101
© 2002 Oxford University Press

Probabilistic alignment of motifs with sequences

Pedro Gonnet 1,* and Frédérique Lisacek 1,2

1 GeneBio S.A., 25. Av. de Champel, 1206 Geneva, Switzerland
2 Laboratoire Genome et Informatique, Tour Evry 2, 91034 Evry Cedex, France

Received on November 20, 2001 ; revised on January 28, 2002 ; accepted on February 15, 2002

Motivation: Motif detection is an important component of the classification and annotation of protein sequences. A method for aligning motifs with an amino acid sequence is introduced. The motifs can be described by the secondary (i.e. functional, biophysical, etc...) characteristics of a signal or pattern to be detected. The results produced are based on the statistical relevance of the alignment. The method was targeted to avoid the problems (i.e. over-fitting, biological interpretation and mathematical soundness) encountered in other methods currently available.

Results: The method was tested on lipoprotein signals in B. subtilis yielding stable results. The results of signal prediction were consistent with other methods where literature was available.

Availability: An implementation of the motif alignment, refining and bootstrapping is available for public use online at http://www.expasy.org/tools/patoseq/

Contact: pedro.gonnet{at}genebio.compedro.gonnet@genebio.com

* To whom correspondence should be addressed.


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