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:
https://redmine.open-bio.org/projects/bioperl/
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.