NAME

Bio::Tools::Analysis::Protein::ELM

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. Two filters can be applied to help limit the rate of false positives: species and cellular compartment of the protein if known. The modules supply methods for setting these attributes. To set 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, as parsed into a data structure, or as Bio::SeqFeature::Generic objects.

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://bio.perl.org/MailList.html           - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

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 _

compartment

 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 selction 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 : none    (retrieves raw text without html)
             a value (retrieves data structure)
             'Bio::SeqFeatureI' (returns array of sequence features)
                                        tag names are : {method=>'ELM', motif=>motifname,
                                     peptide => seqeunce of match,
                                     concensus=> regularexpression of match.
        .
 returns   : see arguments.