/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Coil

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.

_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    :