Bio::Tools::Tmhmm(3) User Contributed Perl Documentation Bio::Tools::Tmhmm(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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
perl v5.14.1 2011-07-22 Bio::Tools::Tmhmm(3)