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
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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.
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://redmine.open-bio.org/projects/bioperl/
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.
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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.