Selenoprofiles is a pipeline for homology-based identification of selenoproteins in nucleotide databases.
The program accepts input alignments of protein sequences (profiles) and combines blast, exonerate and genewise to identify homologous genes. Selenoprofiles uses a modified scoring scheme to align selenocysteine residues. It also comes with built-in profiles for known selenoprotein families, so that it can predict the set of selenoproteins encoded in a target genome out-of-the-box. Selenoprofiles is available for installation in linux based systems.
Main website (including installation instructions): https://genome.crg.es/software/selenoprofiles/
Github page: https://github.com/marco-mariotti/selenoprofiles/
Mariotti M, Guigó R (2010) Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics. 26(21):2656-63.
Santesmasses D, Mariotti M, Guigó R (2018) Selenoprofiles: A Computational Pipeline for Annotation of Selenoproteins. Methods Mol Biol. 1661:17-28.