NAME¶
Bio::Tools::Run::Coil - wrapper for ncoils program
SYNOPSIS¶
# Build a Coil factory
my $factory = Bio::Tools::Run::Coil->new($params);
# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);
DESCRIPTION¶
This module is a wrapper for the
ncoils program available via
<
http://www.russell.embl-heidelberg.de/coils/coils.tar.gz> for
predicting coiled coils in protein sequences.
By default it looks for an executable called
ncoils and data/parameter
files in the directory specified by the
COILSDIR environmental
variable.
REFERENCES¶
Lupas, van Dyke & Stock,
Predicting coiled coils from protein
sequences, Science
252:1162-1164, 1991.
Lupas, A.,
Prediction and Analysis of Coiled-Coil Structures, Meth.
Enzymology
266:513-525, 1996.
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:
http://redmine.open-bio.org/projects/bioperl/
AUTHORS¶
Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
originally written by Marc Sohrmann (ms2@sanger.ac.uk)
Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org> #
Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
program_name¶
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
program_dir¶
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
new¶
Title : new
Usage : $coil->new(@params)
Function: creates a new Coil factory
Returns: Bio::Tools::Run::Coil
Args :
predict_protein_features¶
Title : predict_protein_features()
Usage : DEPRECATED. Use $obj->run instead.
Function: Runs Coil and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
run¶
Title : run
Usage : $obj->run($seq)
Function: Runs Coil and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI, or a Fasta filename.
Title : _input
Usage : obj->_input($seqFile)
Function: Internal(not to be used directly)
Returns :
Args :
_run¶
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An array of Bio::SeqFeature::Generic objects
Args :
_writeSeqFile¶
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns :
Args :