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Bioinformatics Advance Access originally published online on May 12, 2008
Bioinformatics 2008 24(13):1532-1533; doi:10.1093/bioinformatics/btn225
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA

Michiel Van Bel 1,2, Yvan Saeys 1,2 and Yves Van de Peer 1,2,*

1Department of Plant Systems Biology, VIB and 2Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium

*To whom correspondence should be addressed.


  Abstract

Motivation: Many problems in genome annotation are tackled by using a classification model to predict functional sites such as splice sites, translation start sites or stop codons. Locating the correct position of these sites remains one of the most important but also one of the most difficult issues in the structural annotation of genomes. Most of the software currently in use is written for a very specific problem, thereby limiting the possibilities for reuse.

Summary: We developed a software platform that uses a very general approach towards the classification of functional sites in DNA sequences. The program uses an ab initio approach towards the identification of these sites, and extends SpliceMachine, a previously developed splice site predictor that shows state-of-the-art performance for both donor and acceptor splice site recognition in the human and Arabidopsis thaliana genome.

Availability: The program is developed as a stand-alone Java application, and is available as GPLv3 open-source software. The program, source and documentation can be obtained from the ‘Software’ section at http://bioinformatics.psb.ugent.be/

Contact: Yves.VandePeer{at}psb.ugent.be

Supplementary information: Supplementary data is available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on January 25, 2008; revised on January 25, 2008; accepted on May 6, 2008

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