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/.