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my $seq; # a Bio::PrimarySeqI object
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my $tool = Bio::Tools::Analysis::Protein::Scansite->new
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( -seq => $seq->primary_seq(),
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( -seq => $seq->primary_seq );
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# run Scansite prediction on a sequence
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# alternatively you can say
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$tool->seq($seq->primary_seq)->run;
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This class is wrapper around the Scansite 2.0 server which produces
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This class is a wrapper around the Scansite 2.0 server which produces
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predictions for serine, threonine and tyrosine phosphorylation sites
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in eukaryotic proteins. At present this is a basic wrapper for the
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"Scan protein by input sequence" functionality, which takes a sequence
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and searches for motifs. Optionally you can select the search
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strincency as well. At present searches for specific phosphorylation
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sites isn't supported, all predicted sites are returned.
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See L<http://www.scansite.mit.edu/>.
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This inherits Bio::SimpleAnalysisI which hopefully
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makes it easier to write wrappers on various services. This class
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uses a web resource and therefore inherits from Bio::WebAgent.
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and searches for motifs, with the option to select the search
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stringency. At present, searches for specific phosphorylation
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sites are not supported; all predicted sites are returned.
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The Scansite results can be obtained in several formats:
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my $res = $tool->result('');
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$res holds a string of the predicted sites in tabular format.
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my $data_ref = $tool->result('value')
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$data_ref is a reference to an array of hashes. Each element in the
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array represents a predicted phosphorylation site. The hash keys are
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the names of the data fields,i.e.,
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'motif' => 'Casn_Kin1' # name of kinase
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'percentile' => 0.155 # see Scansite docs
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'position' => 9 # position in protein
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'protein' => 'A1' # protein id
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'score' => 0.3696 # see Scansite docs
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'sequence' => 'ASYFDTASYFSADAT' # sequence surrounding site
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'site' => 'S9' # phosphorylated residue
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'zscore' => '-3.110' # see Scansite docs
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my @fts = $tool->Result('Bio::SeqFeatureI');
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which returns an array of L<Bio::SeqFeatureI> compliant objects with
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primary tag value 'Site' and tag names of 'motif', 'score',
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'sequence', 'zscore' as above.
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See L<http://scansite.mit.edu/>.
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This inherits Bio::SimpleAnalysisI which hopefully makes it easier to
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write wrappers on various services. This class uses a web resource and
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therefore inherits from L<Bio::WebAgent>.
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Bioperl modules. Send your comments and suggestions preferably to one
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of the Bioperl mailing lists. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bio.perl.org/MailList.html - About the mailing lists
120
bioperl-l@bioperl.org - General discussion
121
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
79
123
=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep track
82
the bugs and their resolution. Bug reports can be submitted via email
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the bugs and their resolution. Bug reports can be submitted via the
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bioperl-bugs@bio.perl.org
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http://bugzilla.bioperl.org/
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http://bugzilla.open-bio.org/
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package Bio::Tools::Analysis::Protein::Scansite;
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use vars qw(@ISA $FLOAT @STRINGENCY );
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use vars qw($FLOAT @STRINGENCY);
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use HTTP::Request::Common qw (POST);
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use HTTP::Request::Common qw(POST);
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use Bio::SeqFeature::Generic;
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use Bio::Tools::Analysis::SimpleAnalysisBase;
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@ISA = qw(Bio::Tools::Analysis::SimpleAnalysisBase);
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use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
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$FLOAT = '[+-]?\d*\.\d*';
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@STRINGENCY = qw(High Medium Low);
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The method returns a scalar representing a result of an executed
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job. If the job was terminated by an error the result
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job. If the job was terminated by an error, the result may contain
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an error message instead of the real data.
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This implementation returns differently processed data depending on
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Returns a reference to an array of hashes containing the data of one
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phosphorylation site prediction. Key values are :
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phosphorylation site prediction. Key values are:
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motif, percentile, position, protein, score, site, zscore, sequence.
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=head2 stringency
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Usage : $job->stringency(...)
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Usage : $job->stringency(...)
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Returns : The significance stringency of a prediction
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Args : None (retrieves value) or 'High', 'Medium' or 'Low'.
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Purpose : Get/setter of the stringency to be sumitted for analysis.
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$self->{'_stringency'} = $value;
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return $self->{'_stringency'} || $self->input_spec->[4]{'default'} ;
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return $self->{'_stringency'} || $self->input_spec->[2]{'default'} ;
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=head2 protein_id
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Usage : $job->protein_id(...)
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Usage : $job->protein_id(...)
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Returns : The sequence id of the protein or 'unnamed' if not set.
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Purpose : Getter of the seq_id. Returns the display_id of the sequence
336
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$self->{'_result'} = $out_Str;
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$self->{'_parsed'} = \@parsed_Results;
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## is successssful if there are results or if there are no results and
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## is successsful if there are results or if there are no results and
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## this beacuse there are no matches, not because of parsing errors etc.
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$self->status('COMPLETED') if $text ne '' &&
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(scalar @results > 0 ||
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(scalar @results == 0 && $text =~/No sites found/));
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if ($text =~ /server\s+error/i) {
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$self->warn("There was an internal server error !- text below") ;
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sub _process_arguments {
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# extra checking for sequence length
398
# mitoprot specific argument testing
399
my ($self, $args) = @_;
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#use base checking for existence of mandatory fields
401
$self->SUPER::_process_arguments($args);
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# specific requirements
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$self->throw("Sequence must be > 15 amino acids long!")
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if $self->seq->length < 15;
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$self->throw("Sequence must be protein")
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unless $self->seq->alphabet() eq 'protein';
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sub _make_header {
added
removed
Bio/Tools/Analysis/Protein/Scansite.pm
