Bio::Tools::Analysis::UsereContributed PBio::Tools::Analysis::Protein::GOR4(3)NAMEBio::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'}\n";
print "predicted struc at residue 2 is $data_ref->[1]{'struc}\n";
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] ,"\n";
}
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), "\n";
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:
http://bugzilla.open-bio.org/
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 v5.14.12011-0Bio::Tools::Analysis::Protein::GOR4(3)
