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.