[Bioperl-l] run RNAfold in perl

Chris Fields cjfields at uiuc.edu
Mon Nov 26 15:08:24 EST 2007

On Nov 26, 2007, at 1:08 PM, vanam wrote:

> i searches for the embassy version of RNAFOLD (i guess its  
> vrnafold) but i m
> unable to find a downloadable version.all ther is a web interface  
> for it.
> can u tell frm wher to fdownload it????

You will need to install EMBOSS as well as the EMBASSY version of  
VIENNA (something which is documented in the docs that come along  
with the distributions and I will not go into detail on):


This would be your best bet.  Understand that there is no specific  
class framework for dealing with RNA secondary structure in BioPerl,  
so you will be on your own for now.

My suggestion for using Pise had the very important caveats that (1)  
it very well may not work, (2) I have no experience with Pise, let  
alone setting it up locally, therefore (3) I haven't tested it (and  
don't intend to, as I don't have the time).

> or can you just tell me how to set the location in piseapplication to
> localhost n wat to enter in the $email variable????

I have pointed out documentation previously which comes with the  
modules in question.  Remember perldoc is your friend; consulting it  
saves me (and everyone else) time.

 From 'perldoc Bio::Tools::Run::AnalysisFactory::Pise':



Bio::Tools::Run::AnalysisFactory::Pise is a class to create Pise appli-
cation objects, that let you submit jobs on a Pise server.

my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(
                                             -email => 'me at myhome');

The email is optional (there is default one). It can be useful, though.
Your program might enter infinite loops, or just run many jobs: the
Pise server maintainer needs a contact (s/he could of course cancel any
requests from your address...). And if you plan to run a lot of heavy
jobs, or to do a course with many students, please ask the maintainer

The location parameter stands for the actual CGI location, except when
set at the factory creation step, where it is rather the root of all
CGI.  There are default values for most of Pise programs.

You can either set location at:

1 factory creation:
      my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(
                                     -location => 'http://somewhere/ 
                                     -email => 'me at myhome');

2 program creation:
      my $program = $factory->program('water',
                               -location => 'http://somewhere/Pise/ 

3 any time before running:
      $job = $program->run();

4 when running:
      $job = $program->run(-location => 'http://somewhere/Pise/cgi- 

You can also retrieve a previous job results by providing its url:

   $job = $factory->job($url);

You get the url of a job by:




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