Skip Navigation


Bioinformatics Advance Access originally published online on January 29, 2009
Bioinformatics 2009 25(5):674-675; doi:10.1093/bioinformatics/btp020
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
25/5/674    most recent
btp020v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Chapple, C. E.
Right arrow Articles by Krol, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chapple, C. E.
Right arrow Articles by Krol, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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 Médica, 2Centre de Regulació Genómica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain and 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.


  Abstract

Summary: Selenoproteins contain the 21st amino acid selenocysteine which is encoded by an inframe 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 (UTR) 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 scientific communities.

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

Contact: charles.chapple{at}crg.es

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Ivo Hafacker

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
L. Latreche, O. Jean-Jean, D. M. Driscoll, and L. Chavatte
Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine
Nucleic Acids Res., September 1, 2009; 37(17): 5868 - 5880.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.