Bio::Tools::Analysis::Protein::Scansite - a wrapper around the Scansite server
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); }
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.
Bio::SimpleAnalysisI, Bio::WebAgent
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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:
Returns the raw ASCII data stream but without HTML tags
The argument string defined the type of bioperl objects returned in an array. The objects are Bio::SeqFeature::Generic.
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.
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.
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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.