/ 
bioperl-run-1.4
/ Bio::Tools::Run::Tmhmm

NAME

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

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

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://bio.perl.org/MailList.html             - About the mailing lists

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
email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

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, obtiained from ENV variable.
Returns:  string
Args    :

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

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    :