Bio::Tools::Analysis::UsereContributed PeBio::Tools::Analysis::Protein::ELM(3)NAMEBio::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.
perl v5.14.12011-07Bio::Tools::Analysis::Protein::ELM(3)
