debian man page for bio::tools::analysis::protein::elm

Bio::Tools::Analysis::Protein::ELM(3pm) 		User Contributed Perl Documentation		   Bio::Tools::Analysis::Protein::ELM(3pm)

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:

	 https://redmine.open-bio.org/projects/bioperl/

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 v5.14.2							    2012-03-02				   Bio::Tools::Analysis::Protein::ELM(3pm)