Bio::Tools::Analysis::Protein::ELM - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences
# 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);
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.
Bio::SimpleAnalysisI, Bio::WebAgent
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
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/
Richard Adams, Richard.Adams@ed.ac.uk,
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).
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
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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.