bionic (3) Bio::Tools::Analysis::Protein::Sopma.3pm.gz
NAME
Bio::Tools::Analysis::Protein::Sopma - a wrapper around the Sopma protein secondary structure prediction
server
SYNOPSIS
use Bio::Tools::Analysis::Protein::Sopma;
#get a Bio::Seq or Bio::PrimarySeq
my $seq;
my $sopma = Bio::Tools::Analysis::Protein::Sopma->new
(-seq=>$seq, states=>4);
$sopma->run;
print $sopma->result;# #raw text to standard error
DESCRIPTION
A module to remotely retrieve predictions of protein secondary structure. Each residue in the protein
receives a score representing the likelihood of existing in each of four different states (helix, coil,
turn or sheet), e.g.,
my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::Sopma->new
( -seq => $seq,
-states => 4,
-window_width => 15,
);
creates a new object. Compulsory argument -seq. Optional arguments -states,
-window_width,-similarity_threshold. These arguments can also be set by direct methods , e.g.,
$analysis_object->states(4);
$analysis_object->run;
submits the query to the server and obtains raw text output. Given an amino acid sequence the results can
be obtained in 4 formats, determined by the argument to the result method:
1. The raw text of the program output.
my $rawdata = $analysis_object->result;
2. A reference to an array of hashes of scores for each state and the assigned state.
my $data_ref = $analysis_object->result('parsed');
print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n";
print "predicted struc at residue 2 is $data_ref->[1]{'struc}\n";
Hash keys are 'helix', 'struc', 'sheet', 'coil', 'turn'.
3. An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of secondary
structure. Only stretches of helix/sheet predictions for longer than 4 residues are defined as
helices/sheets.
my @fts = $analysis_object->result(Bio::SeqFeatureI);
for my $ft (@fts) {
print " From ", $ft->start, " to ",$ft->end, " struc: " ,
($ft->each_tag_value('type'))[0] ,"\n";
}
4. A Bio::Seq::Meta::Array implementing sequence.
This is a Bio::Seq object that can also hold data about each residue in the sequence. In this case,
the sequence can be associated with a arrays of Sopma prediction scores. e.g.,
my $meta_sequence = $analysis_object->result('meta');
print "scores from residues 10 -20 are ",
$meta_sequence->named_submeta_text("Sopma_helix",10,20), "\n";
Meta sequence names are : Sopma_helix, Sopma_sheet, Sopma_turn, Sopma_coil, Sopma_struc, representing
the scores for each residue.
Many methods common to all analyses are inherited from Bio::Tools::Analysis::SimpleAnalysisBase.
SEE ALSO
Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase Bio::Seq::Meta::Array, 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://github.com/bioperl/bioperl-live/issues
AUTHORS
Richard Adams, Richard.Adams@ed.ac.uk,
APPENDIX
similarity_threshold
Useage : $job->similarity_threshold(...)
Returns : The similarity threshold used in the analysis
Args : None (retrieves value) or an integer (default = 8)
that sets the similarity threshold .
This method gets/sets the similarity threshold for the prediction.
window_width
Usage : $job->window_width(...)
Returns : The window width used in the analysis
Args : None (retrieves value) or an integer (default = 17)
that sets the window width.
This method gets/sets the window width for the prediction, . If attempted to set longer than the
sequence, warns of error.
states
Usage : $job->states(...)
Returns : The number of secondary structure prediction states
Args : None (retrieves value) or either '3' or '4' to set
prior to running analysis.
This method gets/sets the number of states for the prediction, either 3 or 4 (includes turns).
result
Usage : $job->result (...)
Returns : a result created by running an analysis
Args : various
The method returns 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 defines the type of bioperl objects returned in an array. The objects are
Bio::SeqFeature::Generic. Feature primary tag is "2ary". Feature tags are "type" (which can be
helix, sheet coil, or turn if 4 state prediction requested) "method" (Sopma)
'parsed'
Array of hash references of scores/structure assignations { helix => , sheet => , coil => , struc=>}.
'all'
A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class. Meta sequence
names are Sopma_helix, Sopma_sheet, Sopma_coil, Sopma_turn (if defined), and Sopma_struc.