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::TMHMM (3)

.ds Aq ’

NAME

Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes
in a given protein seequence.

CONTENTS

SYNOPSIS



  # Build a Tmhmm  factory

  # $paramfile is the full path to the seg binary file

  my @params = (PROGRAM,$paramfile);
  my $factory = Bio::Tools::Run::Tmhmm->new($param);

  # Pass the factory a Bio::Seq object
  # @feats is an array of Bio::SeqFeature::Generic objects

  my @feats = $factory->run($seq);



DESCRIPTION

Tmhmm is a program for identifying transmembrane helices in proteins.

You must have the environmental variable TMHMMDIR set to the base directory where tmhmm and it’s associated data/option files reside (NOT the bin directory where the actual executable resides)

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



head2 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/



AUTHOR - Bala



 Email savikalpa@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, in this
           case it is the tmhmm installation directory, not the location of
           the executable.
 Returns:  string
 Args    :



    program_path



 Title   : program_path
 Usage   : my $path = $factory->program_path();
 Function: Builds path for executable
 Returns : string representing the full path to the exe
 Args    : none



    new



 Title   : new
 Usage   : $rm->new(@params)
 Function: creates a new Tmhmm factory
 Returns:  Bio::Tools::Run::Tmhmm
 Args    :



    predict_protein_features



 Title   :   predict_protein_features()
 Usage   :   DEPRECATED Use $obj->run($seq) instead
 Function:   Runs Tmhmm and creates an array of featrues
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI



    executable



 Title   : executable
 Usage   : my $exe = $tmhmm->executable(tmhmm);
 Function: Finds the full path to the tmhmm executable
 Returns : string representing the full path to the exe
 Args    : [optional] name of executable to set path to
           [optional] boolean flag whether or not warn when exe is not found



    run



 Title   :   run()
 Usage   :   $obj->run($seq)
 Function:   Runs Tmhmm and creates an array of featrues
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI



    _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::TMHMM (3) 2016-04-05

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