GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::TOOLS::TMHMM (3)

.ds Aq ’

NAME

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

CONTENTS

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



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::TOOLS::TMHMM (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.