[Bioperl-l] Bio::Tools::Primer3 question

Chris Fields cjfields at illinois.edu
Wed Aug 18 00:48:55 EDT 2010


The latest code, along with working tests, is present here:


It needs a few more tests but the initial wrapper tests work fine for primer3 v2.2.1 on both Mac and Linux.  Will try using this to CPAN after a bit more cleanup.


On Aug 17, 2010, at 4:14 PM, Chris Fields wrote:

> Already ahead of you there, unfortunately.  I wrote a complete reimplementation of both the Primer3 parser and the Primer3 wrapper that handles both v1 and v2 of primer3_core.  Lack of tuits lately have prevented me from getting tests written up, so for the time being it's sitting in bioperl-dev:
> http://github.com/bioperl/bioperl-dev
> They are Bio::Tools::Primer3Redux (parser) and Bio::Tools::Run::Primer3Redux (wrapper).
> I rewrote those b/c I found the original modules not adequate enough in many ways for my purposes then (the newer version uses simple features or feature pairs instead of the primer features, for the same reasons you mention re: Tm).  You're more than welcome to hack on the code a bit.  I'm planning on pulling it out into my own github repo for separate submission to CPAN.  
> chris
> On Aug 17, 2010, at 3:50 PM, Hong Xu wrote:
>> Hello all,
>> I'm working to parse the Primer3 release 2.2.2-beta result. I made the
>> necessary changes to make Bio::Tools::Primer3 work with the new output
>> tags of Primer3 release 2.2.2. But when I tried to get the primer Tm,
>> I found that Bio::Tools::Primer3 gave different Tm from Primer3 result
>> file. Then I learned that the Tm was calculated by
>> Bio::SeqFeature::Primer module, not from parsing Primer3 result. If I
>> want to get data from parsing Primer3 result, should I write my own
>> Primer3 parser instead of Bio::Tools::Primer3?
>> thanks a lot,
>> Hong
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