Bio::Tools::Run::Coil(3pm) User Contributed Perl Documentation Bio::Tools::Run::Coil(3pm)
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
<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.
_input
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 :
perl v5.12.3 2011-06-18 Bio::Tools::Run::Coil(3pm)