Bio::Tools::Tmhmm(3) parse TMHMM output (TransMembrane HMM)


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;


TMHMM is software for the prediction of transmembrane helices in proteins. See <> 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


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AUTHOR - Torsten Seemann

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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


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