Ubuntu Manpage: Bio::Tools::Analysis::Protein::Scansite - a wrapper around the Scansite server

Provided by: libbio-perl-perl_1.6.923-1_all

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.

   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.

         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.