Bio::ORA - Olfactory Receptor family Assigner (ORA) [bioperl module]
Take a sequence object from, say, an inputstream, and find an Olfactory Receptor gene. HMM profiles are used in order to identify location, frame and orientation of such gene.
Creating the ORA object, eg:
my $inputstream = Bio::SeqIO->new( -file => 'seqfile', -format => 'fasta' ); my $seqobj = $inputstream->next_seq(); my $ORA_obj = Bio::ORA->new( $seqobj );
Obtain an array holding the start point, the stop point, the DNA sequence and amino-acid sequence, eg:
my $array_ref = $ORA_obj->{'_result'} if ( $ORA_obj->find() );
Display result in genbank format, eg:
$ORA_obj->show( 'genbank' );
Bio::ORA is a featherweight object for identifying mammalian olfactory receptor genes. The sequences should not be longer than 40kb. The returned array include location, sequence and statistic for the putative olfactory receptor gene. Fully functional with DNA and EST sequence, no intron supported.
See Synopsis above for the object creation code.
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::ORA; my $inseq = Bio::SeqIO->new( '-file' => q{<} . $ARGV[0], -format => 'fasta' ); while (my $seq = $inseq->next_seq) { my $ORA_obj = Bio::ORA->new( $seq ); if ( $ORA_obj->find() ) { $ORA_obj->show( 'genbank' ); } else { print {*STDOUT} " no hit!\n"; } }
To use this module you may need: * Bioperl (http://bioperl.org/) modules, * HMMER v3+ distribution (http://hmmer.org/) and * FASTA 36+ distribution (ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/).
This module uses three softwares. If HMMER or FASTA are updated make sure that HMMER's hmmscan and FASTA's tfastx36 and fastx36 still exists under these names. You change the call my editing the "Default softwares" section.
# Default softwares my $hmmscan = 'hmmscan'; my $tfastx = 'tfastx36'; my $fastx = 'fastx36';
If you have any problems with or questions about the scripts, please contact us through a GitHub issue (https://github.com/pseudogene/ora/issues). You are invited to contribute new features, fixes, or updates, large or small; we are always thrilled to receive pull requests, and do our best to process them as fast as we can.
Michael Bekaert (michael.bekaert@stir.ac.uk)
Address: Institute of Aquaculture University of Stirling Stirling Scotland, FK9 4LA UK
perl(1), bioperl web site
Copyright 2007-2016 - Michael Bekaert
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : _findexec Usage : my $path = $self->_findexec( $exec ); Function: Find an executable file in the $PATH. Returns : The full path to the executable. Args : $exec (mandatory) executable to be find.
Title : new Usage : my $nb = Bio::ORA->new( $seqobj, $table, $aug, $hmm ); Function: Initialize ORA object. Returns : An ORA object. Args : $seqobj (mandatory) PrimarySeqI object (dna or rna), $table (optional) translation table/genetic code number, the default value is 1, $aug (optional) use other start codon than AUG (default 0), $hmm (optional) path to hmm profiles by default ORA looks at ./or.hmm.
Title : find Usage : my $bool = $ORI_obj->find( $evalue, $strand, $start, $end ); Function: Identify an olfactory receptor protein. Returns : boolean. Args : $evalue (optional) set the E-value (expected) threshold. Default is 1e-30, $strand(optional) strand where search should be done (1 direct, -1 reverse or 0 both). Default is 0, $start (optional) coordinate of the first nucleotide. Useful for coordinate calculation when first is not 1. Default is 1, $end (optional) coordinate of the last nucleotide. Default is the sequence length.
Title : _what_or Usage : my $bool = $self->_what_or( $strand ); Function: Use HMM profiles to identify an olfactory receptor gene. Returns : boolean. Args : $strand (optional) strand where search should be done (1 direct, -1 reverse or 0 both). Default is 0.
Title : _find_orf Usage : my $bool = $self->_find_or( $strand, $start, $end ); Function: Retrieve the olfactory receptor ORF. Returns : boolean. Args : $strand (mandatory) strand where ORA have been found (1 direct or -1 reverse), $start (mandatory) coordinate of the first nucleotide, $end (mandatory) coordinate of the last nucleotide.
Title : getHits Usage : my @hits = Bio::ORA->getHits( $seq, $evalue, $ref ); Function: Quick localization of ORs (use FASTA). Returns : Array of hits start/stop positions. Args : $seq (mandatory) primarySeqI object (dna or rna), $evalue (mandatory) det the E-value threshold, $ref (optional) path to fasta reference file, by default ORA look at ./or.fasta.
Title : fastScan Usage : my @hits = Bio::ORA->fastScan( $seq, $ref ); Function: Quick localization of ORs (use FASTA). Returns : Array of hits start/stop positions. Args : $seq (mandatory) primarySeqI object (dna or rna), $ref (optional) path to fasta reference file, by default ORA look at ./or.fasta.
Title : show Usage : $ORA_obj->show( $outstyle ); Function: Print result in various style. Returns : none. Args : $outstyle (mandatory) 'fasta', 'genbank', 'cvs', 'xml' or 'tsv' style.
Title : _translation Usage : my ( $start, $end ) = $self->_translation(); Function: format initiation and stop codons for regex. Returns : array with initiation and stop codons. Args : none.
To install Bio::ORA, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ORA
CPAN shell
perl -MCPAN -e shell install Bio::ORA
For more information on module installation, please visit the detailed CPAN module installation guide.