Bio::Tools::Analysis::Protein::Scansite(3pm)		User Contributed Perl Documentation	      Bio::Tools::Analysis::Protein::Scansite(3pm)

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, "
";
	     # 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.

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.

perl v5.14.2							    2012-03-02			      Bio::Tools::Analysis::Protein::Scansite(3pm)