NAME

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

SYNOPSIS

  use Bio::Tools::Analysis::Protein::Sopma;
  #get a Bio::Seq or Bio::PrimarySeq
  my $seq;
  my $sopma = Bio::Tools::Analysis::Protein::Sopma->new
      (-seq=>$seq, states=>4);
  $sopma->run;
  print $sopma->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 four different states (helix, coil, turn or sheet), e.g.,

  my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::Sopma->new
      ( -seq          => $seq,
        -states       => 4,
        -window_width => 15,
      );

creates a new object. Compulsory argument -seq. Optional arguments -states, -window_width,-similarity_threshold. These arguments can also be set by direct methods , e.g.,

  $analysis_object->states(4);
  $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";
    

Hash keys are 'helix', 'struc', 'sheet', 'coil', 'turn'.

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/sheets.

  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 arrays of Sopma prediction scores. e.g.,

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

Meta sequence names are : Sopma_helix, Sopma_sheet, Sopma_turn, Sopma_coil, Sopma_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

  Useage  : $job->similarity_threshold(...)
  Returns : The  similarity threshold used in the analysis
  Args    : None (retrieves value) or  an integer (default = 8) 
            that sets the similarity threshold .

  Usage    : $job->window_width(...)
  Returns  : The window width used in the analysis
  Args     : None (retrieves value) or  an integer (default = 17)
             that sets the window width.

  Usage    : $job->states(...)
  Returns  : The number of secondary structure prediction states
  Args     : None (retrieves value) or either '3' or '4' to set
             prior to running analysis.

  Usage   : $job->result (...)
  Returns : a result created by running an analysis
  Args    : various