NAME

Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)

SYNOPSIS

use Bio::Tools::Tmhmm;
my $parser = Bio::Tools::Tmhmm->new(-fh => $filehandle );
while ( my $tmhmm_feat = $parser->next_result ) {
   # do something, e.g.
   push @tmhmm_feat, $tmhmm_feat;
}

DESCRIPTION

TMHMM is software for the prediction of transmembrane helices in proteins. See http://www.cbs.dtu.dk/services/TMHMM/ for more details.

This module parses the "long output" format of TMHMM 2.0 and creates a Bio:SeqFeature::Generic object for each TMHelix feature found from lines like this:

my_sequence_id  TMHMM2.0  TMhelix     54    76

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Torsten Seemann

Email torsten.seemann AT infotech.monash.edu.au

CONTRIBUTOR - 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 _

new

Title   : new
Usage   : my $obj = Bio::Tools::Tmhmm->new();
Function: Builds a new Bio::Tools::Tmhmm object
Returns : Bio::Tools::Tmhmm
Args    : Either of the following as per L<Bio::Root::IO> interface
            -fh   => $filehandle 
            -file => $filename

next_result

Title   : next_result
Usage   : my $feat = $Tmhmm->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args    : none