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 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. Optionally you can select the search strincency as well. At present searches for specific phosphorylation sites isn't supported, all predicted sites are returned.

See http://www.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://bio.perl.org/MailList.html           - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

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

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.