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Nucleic Acids Research Advance Access originally published online on April 1, 2009
Nucleic Acids Research 2009 37(9):e67; doi:10.1093/nar/gkp215
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Nucleic Acids Research, 2009, Vol. 37, No. 9 e67
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

François-Olivier Desmet1, Dalil Hamroun1,2, Marine Lalande1, Gwenaëlle Collod-Béroud1, Mireille Claustres1,2,3 and Christophe Béroud1,2,3,*

1INSERM, U827, 2CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire and 3Université Montpellier1, UFR Médecine, Montpellier, F-34000, France

*To whom correspondence should be addressed. Tel: +33 4 67 41 53 60; Fax: +33 4 67 41 53 65; Email: christophe.beroud{at}inserm.fr

Received December 11, 2008. Revised February 28, 2009. Accepted March 16, 2009.

Thousands of mutations are identified yearly. Although many directly affect protein expression, an increasing proportion of mutations is now believed to influence mRNA splicing. They mostly affect existing splice sites, but synonymous, non-synonymous or nonsense mutations can also create or disrupt splice sites or auxiliary cis-splicing sequences. To facilitate the analysis of the different mutations, we designed Human Splicing Finder (HSF), a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. It contains all available matrices for auxiliary sequence prediction as well as new ones for binding sites of the 9G8 and Tra2-β Serine-Arginine proteins and the hnRNP A1 ribonucleoprotein. We also developed new Position Weight Matrices to assess the strength of 5' and 3' splice sites and branch points. We evaluated HSF efficiency using a set of 83 intronic and 35 exonic mutations known to result in splicing defects. We showed that the mutation effect was correctly predicted in almost all cases. HSF could thus represent a valuable resource for research, diagnostic and therapeutic (e.g. therapeutic exon skipping) purposes as well as for global studies, such as the GEN2PHEN European Project or the Human Variome Project.


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