NAME¶
Bio::Tools::Analysis::Protein::Scansite - a wrapper around the Scansite server
SYNOPSIS¶
use Bio::Tools::Analysis::Protein::Scansite;
my $seq; # a Bio::PrimarySeqI object
my $tool = Bio::Tools::Analysis::Protein::Scansite->new
( -seq => $seq->primary_seq );
# run Scansite prediction on a sequence
$tool->run();
# alternatively you can say
$tool->seq($seq->primary_seq)->run;
die "Could not get a result" unless $tool->status =~ /^COMPLETED/;
print $tool->result; # print raw prediction to STDOUT
foreach my $feat ( $tool->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 a wrapper around the Scansite 2.0 server which produces
predictions for serine, threonine and tyrosine phosphorylation sites in
eukaryotic proteins. At present this is a basic wrapper for the "Scan
protein by input sequence" functionality, which takes a sequence and
searches for motifs, with the option to select the search stringency. At
present, searches for specific phosphorylation sites are not supported; all
predicted sites are returned.
The Scansite results can be obtained in several formats:
- 1.
- By calling
my $res = $tool->result('');
$res holds a string of the predicted sites in tabular format.
- 2.
- By calling
my $data_ref = $tool->result('value')
$data_ref is a reference to an array of hashes. Each element in the array
represents a predicted phosphorylation site. The hash keys are the names
of the data fields,i.e.,
'motif' => 'Casn_Kin1' # name of kinase
'percentile' => 0.155 # see Scansite docs
'position' => 9 # position in protein
'protein' => 'A1' # protein id
'score' => 0.3696 # see Scansite docs
'sequence' => 'ASYFDTASYFSADAT' # sequence surrounding site
'site' => 'S9' # phosphorylated residue
'zscore' => '-3.110' # see Scansite docs
- 3.
- By calling
my @fts = $tool->Result('Bio::SeqFeatureI');
which returns an array of Bio::SeqFeatureI compliant objects with primary
tag value 'Site' and tag names of 'motif', 'score', 'sequence', 'zscore'
as above.
See <
http://scansite.mit.edu/>.
This inherits Bio::SimpleAnalysisI which hopefully makes 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,
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.
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.
- 'parsed'
- Returns a reference to an array of hashes containing the
data of one phosphorylation site prediction. Key values are:
motif, percentile, position, protein, score, site, zscore, sequence.
stringency¶
Usage : $job->stringency(...)
Returns : The significance stringency of a prediction
Args : None (retrieves value) or 'High', 'Medium' or 'Low'.
Purpose : Get/setter of the stringency to be sumitted for analysis.
protein_id¶
Usage : $job->protein_id(...)
Returns : The sequence id of the protein or 'unnamed' if not set.
Args : None
Purpose : Getter of the seq_id. Returns the display_id of the sequence
object.