NAME¶

Bio::Tools::Analysis::Protein::ELM - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences

SYNOPSIS¶

  # get a Bio::Seq object to start with, or a Bio::PrimaryI object.
  my $tool = Bio::Tools::Analysis::Protein::ELM->
      new(seq => $seqobj->primary_seq() );
  $tool->compartment(['ER', 'Golgi']);
  $tool->species(9606);
  $tool->run;
  my @fts = $tool->Result('Bio::SeqFeatureI');
  $seqobj->addSeqFeature(@fts);

DESCRIPTION¶

This module is a wrapper around the ELM server <http://elm.eu.org/> which predicts short functional motifs on amino acid sequences.

False positives can be limited by providing values for the species and cellular compartment of the protein. To set the species attribute, use either a Bio::Species object or an NCBI taxon ID number. To set the cell compartment attribute (any number of compartments can be chosen) use an array reference to a list of compartment names.

Results can be obtained either as raw text output, parsed into a data structure, or as Bio::SeqFeature::Generic objects.

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,

APPENDIX¶

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

 name        : compartment
 usage       : $elm->compartment(['golgi', 'er']);
 purpose     : get/setter for cell compartment specifications
 arguments   : None, single compartment string or ref to array of
               compartment names.
 returns     : Array of compartment names (default if not previously set).

species¶

 name      : species
 usage     : $tool->species('9606');
 purpose   : get/setter for species selection for ELM server
 arguments : none, taxon_id or Bio::Species object
 returns   : a string of the ncbi taxon_id

result¶

 name      : result
 usage     : $tool->result('Bio::SeqFeatureI');
 purpose   : parse results into sequence features or basic data format
 arguments : 1. none    (retrieves raw text without html)
             2. a value (retrieves data structure)
             3. 'Bio::SeqFeatureI' (returns array of sequence features)
                tag names are : {method => 'ELM', motif => motifname,
                                 peptide => seqeunce of match,
                                 concensus => regexp of match}.
 returns   : see arguments.