Re: [DIYbio] Designing primers for PCR

Whoops, forgot this iGEM code:
https://github.com/russelldurrett/NYC_iGEM/tree/master/Hannah's%20Primer%20Designer/biopython

it looks really bloated (it needs SQL), but maybe you can pull some
stuff from it

On Fri, Feb 8, 2013 at 6:48 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
> On Fri, Feb 8, 2013 at 12:47 AM, Mega <masterstorm123@gmail.com> wrote:
>> Hi everyone,
>>
>>
>> I'm trying to design primers on my own. but now there are a few questions
>> that Google couldn't answer me.
>>
>
> Do you know how to use Python? You should probably start messing with
> bioPython.... You can spin your own primer design code that way
>
> Here's a good quick overview of the things you need to watch for
> during primer design
> http://instructional1.calstatela.edu/jmomand2/2004/programming/ppt/chan_ronny.ppt
> it says:
> Primer length
> Melting Temperature
> GC content
> Hair-pin loop
> Self-dimerization
> Cross-dimerization
>
> The main thing you need to look at is melting temp calculations:
> http://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-module.html#Tm_staluc
>
> and this code extends the nearest neighbor Tm calculation with
> monovalent ion, Mg2+, dNTP, DNA, and DMSO corrections (references in
> the code)
> http://pastebin.com/PijkvZr5
>
> here are some primer tools that may or may not be good, I haven't
> looked through the code to see, and I haven't tested it:
> http://sourceforge.net/projects/pythia/
>
> This bioPython introduction has tutorials on how to use it with
> Primer3 (starting around 2/3rd the way through the PDF), all right out
> of the box:
> http://www.biopython.org/DIST/docs/presentations/biopython.pdf
>
> --
> -Nathan



--
-Nathan

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