Bio::Tools::Analysis::Protein::NetPhos(3)

NAME
Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server

SYNOPSIS
  use Bio::Tools::Analysis::Protein::NetPhos;

  my $seq; # a Bio::PrimarySeqI object
  my $threshold  = "0.90";

  my $netphos = Bio::Tools::Analysis::Protein::NetPhos->new
     ( -seq => $seq,
       -threshold => $threshold );

  # run NetPhos prediction on a sequence
  my $netphos->run();

  # alternatively you can say
  $netphos->seq($seq)->threshold($threshold)->run;

  die "Could not get a result" unless $netphos->status =~ /^COMPLETED/;

  print $netphos->result;     # print raw prediction to STDOUT

  foreach my $feat ( $netphos->result('Bio::SeqFeatureI') ) {

      # do something to SeqFeature
      # e.g. print as GFF
      print $feat->gff_string, "\n";
      # or store within the sequence - if it is a Bio::RichSeqI
      $seq->add_SeqFeature($feat)

 }

DESCRIPTION
This class is wrapper around the NetPhos 2.0 server which produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.

See <http://www.cbs.dtu.dk/services/NetPhos/>.

This the first implementation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class uses a web resource and therefore inherits from Bio::WebAgent.

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

AUTHORS
Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

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    : none (but an implementation may choose
           to add arguments for instructions how to process
           the raw result)

The method returns a scalar representing 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 (or both, depending on the implementation).

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 defined the type of bioperl objects returned in an array. The objects are Bio::SeqFeature::Generic.

anything else
    Array of array references of [ position, score, residue].

  threshold
 Usage   : $job->threshold(...)
 Returns  : The significance threshold of a prediction
 Args     : None (retrieves value) or a value between 0 and 1.
 Purpose  : Get/setter of the threshold to be sumitted for analysis.