Provided by: libbio-perl-perl_1.6.901-2_all bug


       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

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

       See <>

       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,, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org


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