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