Bio::Tools::Analysis::Protein::Scansite(3) 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.

Return formats

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.

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. 

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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, [email protected],

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.

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