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Christopher Fields
and 1 contributors


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',

  my $ese_finder = Bio::Tools::Analysis::DNA::ESEfinder->
      new(-seq => $seq);

  # run ESEfinder prediction on a DNA sequence

  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



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://exon.cshl.org/ESE/index.html

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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Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:



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 _