I'm thinking of a website which is an online tool that you can use to calculate effective reactions for your PCR. It would have different modes, optimizing the reaction for different purposes:
- Cloning
- Detection/forensics/diagnostics
- Size verification
- Very long template
- GC rich template
And so on. Ideally you would enter primer sequences, and it would take care of everything like optimizing annealing temperature automatically. It would come with the details of many commercial PCR enzyme kits pre-loaded into its database, so you can just pick, say, "Phusion Pfu" and have it load up the appropriate buffers and so on automatically (perhaps even suggest homemade buffers in case you don't have the correct one). It would be able to suggest things like alternative DMSO or Betaine recipes if you indicate that you have these available.
Obviously PCR optimiziation is impossible to do 100% right without some trial and error, but this tool wouldn't be trying for that. It would just give you a very educated guess for a first-step recipe by leveraging the published research.
To give a more concrete idea of what I want, see this utility for calculating centrifuge speeds: http://www.geneinfinity.org/sp/sp_rotor.html
As you can see, the RCF conversion isn't a complicated calculation, but the really nice part of the site is that it knows all the different rotors you might have in your lab, so you don't have to hunt for the manual yourself.
I would like something like this for PCRs. Does such a website exist (I couldn't find much with Google)? Does such an online tool, free or proprietary, exist? If no, are there any fundamental theoretical problems that would preclude the existence of one, or is it just that nobody bothered?
