NAME¶

Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder server

SYNOPSIS¶

  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)
  }

DESCRIPTION¶

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.

1.

"$ese_finder->result('')" retrieves the raw text output of the program

2.

"$ese_finder->result('all')" returns a Bio::Seq::Meta::Array object with prediction scores for all residues in the sequence

3.

"$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

4.

"$ese_finder->result('raw')" returns an array of significant matches with each element being a reference to [SR_protein, position, motif, score]

See <http://rulai.cshl.edu/tools/ESE2/>

This the second implementation 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.

SEE ALSO¶

Bio::SimpleAnalysisI, Bio::WebAgent

FEEDBACK¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://github.com/bioperl/bioperl-live/issues

AUTHORS¶

Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

APPENDIX¶

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _