Provided by: libbio-perl-perl_1.7.2-3_all bug


       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']);
         my @fts = $tool->Result('Bio::SeqFeatureI');


       This module is a wrapper around the ELM server <> 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


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       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 selection 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.