Journal Article

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

Charles E. Chapple, Roderic Guigó and Alain Krol

in Bioinformatics

Volume 25, issue 5, pages 674-675
Published in print March 2009 | ISSN: 1367-4803
Published online January 2009 | e-ISSN: 1460-2059 | DOI:

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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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1271 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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