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 = new Bio::PrimarySeq
  (-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

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.