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Christopher Fields
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Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server


  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

  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



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 implentation 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.


Bio::SimpleAnalysisI, Bio::WebAgent


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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
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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:



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


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    : 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:


Returns the raw ASCII data stream but without HTML tags


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].


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