title: SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  SECISaln is freely available as a web-based tool at http://genome.crg.es/software/secisaln/.
authors.affiliation: Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain. charles.chapple@crg.es
authors.forename: Charles E
authors.initials: CE
authors.lastname: Chapple
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.forename: Alain
authors.initials: A
authors.lastname: Krol
mesh_terms: D020413:3' Untranslated Regions / Q000737:chemistry*; D001483:Base Sequence; D018388:Codon, Terminator; D019295:Computational Biology / Q000379:methods*; D005057:Eukaryotic Cells / Q000502:physiology; D020407:Internet; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry; D051140:Selenoproteins / Q000737:chemistry / Q000235:genetics*; D012984:Software
chemical_list: D020413:3' Untranslated Regions; D018388:Codon, Terminator; D051140:Selenoproteins; D012313:RNA