SECISearch3 and Seblastian: prediction of SECIS elements and selenoproteins
Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3′ UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins.
In this webserver (go to http://seblastian.crg.es) we provide public access to two new computational methods for selenoprotein identification and analysis: SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins.
A open-access paper describing these methods, including their validation and the prediction of new selenoproteins in many eukaryotic lineages, was published in Nucleic Acid Research: http://nar.oxfordjournals.org/content/early/2013/06/19/nar.gkt550.full
This project is the result of a collaboration with Vadim Gladyshev's lab in Harvard (http://gladyshevlab.bwh.harvard.edu/).