[Bioperl-l] Primer3.pm

Rob Edwards rob at salmonella.org
Tue Mar 29 11:31:56 EST 2005

Bio::Tools::Run::Primer3 is the interface to run the primer3 program. 
Bio::Tools::Primer3 is the interface to parse the output from primer3.

If you already have run primer3 (or do it outside bioperl) then you 
don't need the run module, you can use the parsing module and pass in 
the file. If you want to take a sequence object, design primers against 
it using primer3, and get sequence objects back for the primers and the 
products then you need both.


On Mar 29, 2005, at 5:43 AM, Mike Muratet wrote:

> On Tue, 29 Mar 2005, Mike Muratet wrote:
>> Greetings
>> I know this has come up before, but I can't seem to track down the 
>> answer.
>> There is a Primer3.pm in Bio/Tools. The latest 1.4 module docs on the 
>> web
>> page place it there. It's also in Bio/Tools/Run through 
>> bioperl-run-1.4.
>> Which is the correct (or best) path/version to use?
>> thanks
>> Mike
> Hello again
> A careful reading of the documentation for each module would indicate 
> that
> the former above is called by the latter which is probably the answer 
> to
> the question unless someone knows otherwise. There is nothing in the 
> docs
> on the bioperl webpage for Bio/Tools/Run/Primer3.pm.
> Mike
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