debian man page for bio::tools::run::coil

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)