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Bio::Tools::Analysis::Protein::NetPhos.3pm

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 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.

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:

   http://bugzilla.open-bio.org/
 
 

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 beween 0 and 1.
  Purpose  : Get/setter of the threshold to be sumitted for analysis.