debian man page for bio::tools::analysis::dna::esefinder

Bio::Tools::Analysis::DNA::ESEfinder(3pm)		User Contributed Perl Documentation		 Bio::Tools::Analysis::DNA::ESEfinder(3pm)

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, "
";
	     # 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 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.

SEE ALSO
       Bio::SimpleAnalysisI, Bio::WebAgent

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   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:

	 https://redmine.open-bio.org/projects/bioperl/

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 _

perl v5.14.2							    2012-03-02				 Bio::Tools::Analysis::DNA::ESEfinder(3pm)