GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::TOOLS::RUN::COIL (3)

.ds Aq ’

NAME

Bio::Tools::Run::Coil - wrapper for ncoils program

CONTENTS

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 <B>ncoilsB> 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 <B>252B>:1162-1164, 1991.

Lupas, A., Prediction and Analysis of Coiled-Coil Structures, Meth. Enzymology <B>266B>: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    :



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::TOOLS::RUN::COIL (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.