Provided by: libbio-perl-perl_1.6.901-2_all bug

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.