Bio::Tools::Run::Coil.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

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://bugzilla.open-bio.org/
 
 

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    :