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Bioinformatics Advance Access published online on January 29, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp020
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© 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.

SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements

Charles E. Chapple 1,*, Roderic Guigó 1,2 and Alain Krol 3

1Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
2Centre de Regulació Genòmica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
3Unité Architecture et Réactivité de l'ARN, Université Louis Pasteur de Strasbourg, CNRS, 15 rue René Descartes, F-67084 Strasbourg, France

*To whom correspondence should be addressed. Mr. Charles Chapple, E-mail: charles.chapple{at}crg.es


  Abstract

Summary: Selenoproteins contain the 21st amino acid selenocysteine which is encoded by an in-frame UGA codon, usually read as a stop. In eukaryotes, its co-translational recoding requires the presence of an RNA stem-loop structure, the SECIS element in the 3 Untranslated Region of selenoprotein mRNAs. Despite little sequence conservation, SECIS elements share the same overall secondary structure. Until recently, the lack of a significantly high number of selenoprotein mRNA sequences hampered the identification of other potential sequence conservation. In this work, the web based tool SECISaln provides for the first time an extensive structure-based sequence alignment of SECIS elements resulting from the well-defined secondary structure of the SECIS RNA and the increased size of the eukaryotic selenoproteome. We have used SECISaln to improve our knowledge of SECIS secondary structure and to discover novel, conserved nucleotide positions and we believe it will be a useful tool for the selenoprotein and RNA scienti.c communities.

Availability: SECISaln is freely available as a web based tool at http://genome.crg.es/software/secisaln/.

Contact: charles.chapple{at}crg.es

Associate Editor: Prof. Ivo Hofacker

Received on October 7, 2008; revised on December 18, 2008; accepted on January 7, 2009

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[Abstract] [Full Text] [PDF]


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