++ed by:
THALJEF FIBO CJFIELDS GENEHACK MAJENSEN

5 PAUSE user(s)
6 non-PAUSE user(s).

Christopher Fields
and 1 contributors

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 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://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 _