19 Aug 18:55
Bioperl Primer3 Tm calculation of a pre-defined primer
From: XQ Xu <xxq.t.xu <at> gmail.com>
Subject: Bioperl Primer3 Tm calculation of a pre-defined primer
Newsgroups: gmane.comp.lang.perl.bio.general
Date: 2008-08-19 16:57:41 GMT
Subject: Bioperl Primer3 Tm calculation of a pre-defined primer
Newsgroups: gmane.comp.lang.perl.bio.general
Date: 2008-08-19 16:57:41 GMT
Hi all, I'm using Primer3 to design primers (Bio::Tools::Primer3). I also need use Primer3 to calculate Tm for some pre-defined primers; however there is no direct way to calculate Tm with Primer3. I have to call Primer3 and supply a pre-defined primer, a template, etc to let it run and hopefully Primer3 finds a pair of primers for me, then I have to open the output and find out what the Tm is for my pre-defined primer. Do I miss any function that can do this quickly for me? I know there's another module (Bio::SeqFeature::Primer) can do this quickly, but the Tm is calculated with different parameters; therefore it's not good to use it while I use Primer3 to design primers. Any input? Thanks! -Tony
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