Provided by: libbio-perl-run-perl_1.6.9-1_all bug

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    :