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::GOR4(3pm) User Contributed Perl Documentation Bio::Tools::Analysis::Protein::GOR4(3pm)NAME
Bio::Tools::Analysis::Protein::GOR4 - a wrapper around GOR4 protein secondary structure prediction server
SYNOPSIS
use Bio::Tools::Analysis::Protein::GOR4;
#get a Bio::Seq or Bio::PrimarySeq
use Bio::PrimarySeq;
$seq = Bio::PrimarySeq->new
(-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
-primary_id=>'test'); # a Bio::PrimarySeqI object
my $gor4 = Bio::Tools::Analysis::Protein::GOR4->new (-seq=>$seq);
$gor4->run;
print $gor4->result;# #raw text to standard error
DESCRIPTION
A module to remotely retrieve predictions of protein secondary structure. Each residue in the protein receives a score representing the
likelihood of existing in each of three different states (helix, coil or sheet), e.g.,
my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::GOR4->
new(-seq => $seq);
creates a new object
$analysis_object->run;
submits the query to the server and obtains raw text output
Given an amino acid sequence the results can be obtained in 4 formats, determined by the argument to the result method
1. The raw text of the program output
my $rawdata = $analysis_object->result;
2. An reference to an array of hashes of scores for each state and the assigned state.
my $data_ref = $analysis_object->result('parsed');
print "score for helix at residue 2 is $data_ref->[1]{'helix'}
";
print "predicted struc at residue 2 is $data_ref->[1]{'struc}
";
3. An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of secondary structure. Only stretches of
helix/sheet predictions for longer than 4 residues are defined as helices. See Bio::Tools::Analysis::Domcut.pm for examples of how to
add sequence features.
my @fts = $analysis_object->result(Bio::SeqFeatureI);
for my $ft (@fts) {
print " From ", $ft->start, " to ",$ft->end, " struc: " ,
($ft->each_tag_value('type'))[0] ,"
";
}
4. A Bio::Seq::Meta::Array implementing sequence.
This is a Bio::Seq object that can also hold data about each residue in the sequence In this case, the sequence can be associated with
a single array of GOR4 prediction scores. e.g.,
my $meta_sequence = $analysis_object->result('all');
print "helix scores from residues 10-20 are ",
$meta_sequence->named_submeta_text("GOR4_helix",10,20), "
";
Meta sequence names are : GOR4_helix, GOR4_sheet, GOR4_coil, GOR4_struc, representing the scores for each residue.
Many methods common to all analyses are inherited from Bio::Tools::Analysis::SimpleAnalysisBase.
SEE ALSO
Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Seq::Meta::Array, 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
Name : result
Usage : $job->result (...)
Returns : a result created by running an analysis
Args : see keys of $RESULT_SPEC
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 "2ary". Feature tags are "type" (which can be helix, sheet or coil) "method" (GOR4).
'parsed'
Array of hash references of { helix =>, sheet => , coil => , struc=>}.
'meta'
A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class. Meta sequence names are GOR4_helix, GOR4_sheet,
GOR4_coil, GOR4_struc.
perl v5.14.2 2012-03-02 Bio::Tools::Analysis::Protein::GOR4(3pm)