Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins UGA is recoded to Sec in presence of specific signals on selenoprotein gene transcripts. Due to the dual role of the UGA codon, gene prediction programs fail to predict correctly selenoproteins. Selenoprofiles is an homology-based in silico tool able to scan genomes for members of the known selenoprotein families, thus finding both selenoproteins and cysteine homologues. Selenoprofiles is built in python, and it internally runs psitblastn, exonerate, genewise and SECISearch.
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Mariotti M, Guigo R
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes.
Bioinformatics. 2010 Nov 1;26(21):2656-63. Epub 2010 Sep 21