Selenoprofiles

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. Selenoprofiles can be used with no human intervention at all, although we recommend a manual (and expert) revision of results. Currently, Selenoprofiles is tuned to search only eukaryotic sequences, and includes profile alignments for each known eukaryotic selenoprotein and selenocysteine-related family. You can request an analysis with Selenoprofiles by sending an email to marco.mariotti at crg.es , or you can install the program yourself by following the instructions below.

The Selenoprofiles predictions on Ensembl genomes are available through a DAS server at http://genome.crg.cat:9000/das

A graphical summary of said predictions can be downloaded here: http://genome.crg.es/datasets/selenoprofiles2010/results_ensembl52.png  

Contact: marco.mariotti@crg.es

INSTALLATION

The first step to install Selenoprofiles is to unzip all files in this tarball to what will be your Selenoprofiles installation directory. Then, all external programs that Selenoprofiles utilizes must be manually installed. Selenoprofiles looks for executables in the folder defined by the "-bin_folder" option, which by default is the installation directory. So after installing the following programs you have to link the executables there. For Selenoprofiles to be working, these executables must be present (program packages are indicated in parenthesis): blastall (from ncbi blast package 2.2.22) blastpgp (from ncbi blast package 2.2.22) formatdb (from ncbi blast package 2.2.22) exonerate (from exonerate version 2.2.0) fastafetch (from exonerate version 2.2.0) fastaindex (from exonerate version 2.2.0) fastasubseq (from exonerate version 2.2.0) fastalength (from exonerate version 2.2.0) genewise (from Wise2 package) For genewise, a particular procedure has to be done to make possible using a custom scoring matrix that takes into account the UGA as selenocysteine. Once you finished the genewise installation, copy the whole wisecfg directory in a new directory called wisecfg inside the selenoprofiles installation directory should be fine). Then replace two files (codon.table and BLOSUM62sel.bla) with the files found in the selenoprofiles package.

When all programs are ready to use, we proceed to prepare the selenoprofiles.config file. In the file you downloaded, you'll find a number of INSTALL_DIR occurences. If everything worked out, now you just have to substitute these occurences with your Selenoprofiles installation path and you then can launch selenoprofiles.py

MANUAL

You can download the last version of selenoprofiles manual here: http://genome.crg.es/~mmariotti/selenoprofiles_manual.txt