Bio::Tools::Analysis::Protein::ELM.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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

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:
   http://bugzilla.open-bio.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 : 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.