bio::tools::analysis::protein::elm(3pm) [debian man page]
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)
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Bio::Tools::Analysis::Protein::Mitoprot(3pm) User Contributed Perl Documentation Bio::Tools::Analysis::Protein::Mitoprot(3pm) NAME
Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot server SYNOPSIS
use Bio::Tools::Analysis::Protein::Mitoprot; use Bio::PrimarySeq; my $seq = Bio::PrimarySeq->new (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL', -primary_id=>'test'); # a Bio::PrimarySeqI object my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new ( -seq => $seq ); # sequence must be >!5aa long and start with an M. # run Mitoprot prediction on a DNA sequence my $mitoprot->run(); die "Could not get a result" unless $mitoprot->status =~ /^COMPLETED/; print $mitoprot->result; # print raw prediction to STDOUT foreach my $feat ( $mitoprot->result('Bio::SeqFeatureI') ) { # do something to SeqFeature # e.g. print as GFF print $feat->gff_string, " "; # or store within the sequence - if it is a Bio::RichSeqI $seq->add_SeqFeature($feat); } DESCRIPTION
This class is a wrapper around the Mitoprot web server which calculates the probability of a sequence containing a mitochondrial targetting peptide. See http://mips.gsf.de/cgi-bin/proj/medgen/mitofilter for more details. The results can be obtained in 3 formats: 1. The raw text of the program output my $rawdata = $analysis_object->result; 2. An reference to a hash of scores : my $data_ref = $analysis_object->result('parsed'); print "predicted export prob is $data_ref->{'export_prob'} "; # key values of returned hash are input_length, basic_aas, acidic_aas, export_prob, charge, cleavage_site. 3. A Bio::SeqFeature::Generic object my $ft = $analysis_object->result(Bio::SeqFeatureI); print "export prob is ", ($ft->each_tag_value('export_prob'))[0] ," "; This the second implentation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class uses a web resource and therefore inherits from Bio::WebAgent. SEE ALSO
Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, 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 _ result Usage : $job->result (...) Returns : a result created by running an analysis Args : various The method returns a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data. This implementation returns differently processed data depending on argument: undef Returns the raw ASCII data stream but without HTML tags 'Bio::SeqFeatureI' The argument string defines the type of bioperl objects returned in an array. The objects are Bio::SeqFeature::Generic. Feature primary tag is "SigSeq". Feature tags are input_length , basic_aas, acidic_aas, export_prob, charge, cleavage_site, method. 'parsed' hash references of parsed results { input_length =>, basic_aas=>, acidic_aas=>, export_prob=>, charge=>, cleavage_site=>}. perl v5.14.2 2012-03-02 Bio::Tools::Analysis::Protein::Mitoprot(3pm)