Optional experiment - Manganese + MyTaq Red for mutagenesis

[ericmjl]

We've got manganese chloride (MnCl₂) borrowed from the Dedon lab. Also have MnSO₄ ordered in.

1. Make up 10 mM stock solution of MnCl₂.
2. Set up PCRs (say, PB2 Part 2, which is well within what we can sequence in one Sanger reaction) with 0-5 mM final concentration of MnCl₂, in increments of 0.5 mM.
3. We'll send the PCR products for sequencing, and analyze the Sanger traces.

A possible set of analyses that can be answered from this is:

• Within a defined start and stop region, what is the number of positions that have mixed peaks as a function of Mn²⁺ concentration? What does the curve look like? (Tables are not helpful... yet most protocols only provide tables...)
• What is the mutational bias, as measured by the ratio of trace peaks?

Because this is a new experiment, we should create a new folder under experiments, with a new start date in the folder name - maybe YYYYMMDD-taqhack?

[ericmjl]

@Starnite: just added hacky taq code! check it out under "experiments".

I've labelled it a "temp" folder for now. It'll probably help you get up and running with your own code - you can build on top of it to do more sophisticated analyses if you so choose to.