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Bioinformatics Advance Access published online on March 4, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp124
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans

Francesco Piva *, Matteo Giulietti , Linda Nocchi and Giovanni Principato

Institute of Biology and Genetics, Polytechnic University of Marche, 60131, Ancona, ITALY.

*To whom correspondence should be addressed. Dr. Francesco Piva, E-mail: f.piva{at}univpm.it


  Abstract

Summary: The correct post-transcriptional RNA processing is finely regulated by RNA-binding proteins. Unfortunately there is little experimental information on target RNA sequences of RNA-binding proteins and moreover such experimentally derived target sequences are annotated in a compact form by the score matrices that overestimate the number of possible recognized sequences. We carried out an exhaustive hand curated literature search to create a database, SpliceAid, collecting all the experimentally assessed target RNA sequences that are bound by splicing proteins in humans. We built a web resource, database driven, to easy query SpliceAid and give back the results by an accurate and dynamic graphic representation.

Availability: SpliceAid database is freely accessible at http://www.introni.it/splicing.html

Contact: f.piva{at}univpm.it

Associate Editor: Prof. Alfonso Valencia

Received on October 14, 2008; revised on January 29, 2009; accepted on February 27, 2009

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