Selenoprofiles 3

Posted Fri, 2013-05-17 03:07 by Marco Mariotti

Selenoprofiles is a pipeline for profile-based protein finding in genomes.

Provided one or more protein alignments, it scans a target genome (or any other nucleotide database) and reports the gene structures of homologous genes. It can be used to easily characterize any protein family of interest across a massive amount of sequenced genomes, allowing a finely tuned filtering of results. Or it can be used with comprehensive sets of input profiles, in order to completely annotate by homology one or more genomes. The pipeline runs internally blast (psitblastn), exonerate (p2g mode) and genewise, combining them into a final set of non-overlapping predictions for all profiles.

Selenoprofiles is highly flexible. Even unexperienced user can edit the procedures of filtering, adapting them for each profile. The advanced user can plug-in its own code to customize the internal procedures of labelling, filtering, solving overlaps, outputing. It is also possible to write code to annotate genomic features of the predicted gene, such as protein or RNA motifs, which are stored and added to the native selenoprofiles output.

Although the program offers a variety of filtering methods, the default filter is quite effective. For each candidate, a measure of its similarity with the sequences in the profile is computed (AWSI score, see manual). The resulting score is compared to the distribution of this measure within the profile sequences. In this way, very conserved alignment profiles allow only highly similar sequences to pass the filter and be output.

Selenoprofiles can be used with any input protein family, but we initially developed it for selenoproteins. These peculiar proteins contain a selenocysteine, the 21st amino acid, which is inserted in correspondence to specific UGA codons, normally signalling translation termination. In selenoprotein transcripts we find specific secondary structures (SECIS elements), which targets a specific UGA to be read as Sec instead that as a stop. Since selenoproteins possess this peculiar feature (recoding of specific stop codons), normal gene prediction programs fail to predict them. Selenoprofiles in contrast can correctly predict selenoprotein genes, by using technical expedients to align selenocysteine positions. Selenoprofiles includes built-in profiles for selenoproteins and other proteins related to selenocysteine, allowing out-of-the-box prediction of these families.

Citation

Mariotti M, Guigó R. Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics. 2010 Nov 1;26(21):2656-63. Epub 2010 Sep 21

(Note that the paper refers to outdated version 1)

Installation

All "slave" programs run by selenoprofiles must be installed by user:

Blast: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ [blastall legacy suite required (2.2.2x). Blast+ programs are not supported yet]
Exonerate: http://www.ebi.ac.uk/~guy/exonerate/
Genewise: ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
Mafft: http://mafft.cbrc.jp/alignment/software/

If you experience problems in the installation of these programs, this page may help you. Selenoprofiles can be installed on any unix system with python 2.6 or newer. A python command line installer (install_selenoprofiles.py) is provided inside the installation package that you can find below. The tar package contains also the manual which is linked below.

Download selenoprofiles 3 installation package

Download selenoprofiles manual

Follow the instructions on the README file included in the package. To be used with the built-in profiles, Selenoprofiles requires a few accesory files. These include the large ncbi nr database. This used with blastp to query with sequences of candidates, to assign a filtering score based on the titles of the blastp matches. If you plan to use selenoprofiles only with your own custom profiles, you can skip its download by performing a minimal installation with:

python install_selenoprofiles.py -min

Output and accessory programs

Several output formats are available, such as gff or fasta for nucleotide or protein sequences. The manual explains how to activate the built-in output types, and how to customize output by adding information of interesdt. By default, selenoprofiles produce only two type of output files: a fasta alignment of all predictions aligned to their corresponding profile, and a human readable p2g file showing the alignment gene structure and sequence (find an example of p2g file in here). The selenoprofiles package then contains a few additional programs, suited for projects aimed at searching certain protein families in many target species. The program selenoprofiles_join_alignments retrieves and merge into a single alignment all the results in different species. Then, selenoprofiles_tree_drawer allows their visualization in the phylogenetic tree of the target species. This program require the installation of the python tree environment ete2: http://ete.cgenomics.org/. Selenoprofiles_tree_drawer can generate images like those below.

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