Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder server
use Bio::Tools::Analysis::DNA::ESEfinder; use strict; my $seq; # a Bio::PrimarySeqI or Bio::SeqI object $seq = Bio::Seq->new( -primary_id => 'test', -seq=>'atgcatgctaggtgtgtgttttgtgggttgtactagctagtgat'. -alphabet=>'dna'); my $ese_finder = Bio::Tools::Analysis::DNA::ESEfinder-> new(-seq => $seq); # run ESEfinder prediction on a DNA sequence $ese_finder->run(); die "Could not get a result" unless $ese_finder->status =~ /^COMPLETED/; print $ese_finder->result; # print raw prediction to STDOUT foreach my $feat ( $ese_finder->result('Bio::SeqFeatureI') ) { # do something to SeqFeature # e.g. print as GFF print $feat->gff_string, "\n"; # or store within the sequence - if it is a Bio::SeqI $seq->add_SeqFeature($feat) }
This class is a wrapper around the ESEfinder web server which uses experimentally defined scoring matrices to identify possible exonic splicing enhancers in human transcripts.
The results can be retrieved in 4 ways.
$ese_finder->result('') retrieves the raw text output of the program
$ese_finder->result('')
$ese_finder->result('all') returns a Bio::Seq::Meta::Array object with prediction scores for all residues in the sequence
$ese_finder->result('all')
$ese_finder->result('Bio::SeqFeatureI') returns an array of Bio::SeqFeature objects for sequences with significant scores. Feature tags are score, motif, SR_protein and method
$ese_finder->result('Bio::SeqFeatureI')
$ese_finder->result('raw') returns an array of significant matches with each element being a reference to [SR_protein, position, motif, score]
$ese_finder->result('raw')
See http://rulai.cshl.edu/tools/ESE2/
This the second implentation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class uses a web resource and therefore inherits from Bio::WebAgent.
Bio::SimpleAnalysisI, Bio::WebAgent
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Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
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