Bio::Tools::Analysis::Protein::ELM # 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. Two filters can be applied to help limit the rate of false positives: species and cellular compartment of the protein if known. The modules supply methods for setting these attributes. To set 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, as parsed into a data structure, or as Bio::SeqFeature::Generic objects. Bio::SimpleAnalysisI, Bio::WebAgent

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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.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 _

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). 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 : none (retrieves raw text without html) a value (retrieves data structure) 'Bio::SeqFeatureI' (returns array of sequence features) tag names are : {method=>'ELM', motif=>motifname, peptide => seqeunce of match, concensus=> regularexpression of match. . returns : see arguments.