NAME

Bio::Tools::Analysis::Protein::HNN - a wrapper around the HNN protein secondary structure prediction server

SYNOPSIS

  use   Bio::Tools::Analysis::Protein::HNN;
  #get a Bio::Seq or Bio::PrimarySeq
  use Bio::PrimarySeq;
  my $seq = Bio::PrimarySeq->new
      (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
       -primary_id=>'test'); # a Bio::PrimarySeqI object
  my $hnn = Bio::Tools::Analysis::Protein::HNN->new (-seq=>$seq);
  $hnn->run;
  print $hnn->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::HNN->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.

A 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.

  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 HNN prediction scores. e.g.,

  my $meta_sequence = $analysis_object->result('meta');
  print "helix scores from residues 10-20 are ",
      $meta_sequence->named_submeta_text("HNN_helix",10,20), "\n";
    

Meta sequence default names are : HNN_helix, HNN_sheet, HNN_coil, HNN_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

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://github.com/bioperl/bioperl-live/issues

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 _

 NAme    : result
 Usage   : $job->result (...)
 Returns : a result created by running an analysis
 Args    : see keys of $INPUT_SPEC