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 $netphos->seq($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) } 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

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki@ebi.ac.uk 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: 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. 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.