Warning

Matteo just upgraded both Bootstrap and Font Awesome, and did a major change to the Mako templating so bugginess is a given.

Note

Herein are some small scripts of no value written main for style experimenting.

Pedel

Mini-Pedel from PCR: failure

Predicted diversity (PCR mini-Pedel)

Description

Normal pedel is server-side Python/C++, here it is JS. Strategising for more responsive element...

The PCR starting point is cool, but best just make a modal calculator.

Roghly predict the mutation load from a PCR reaction based on the template and yields or predict a target template concentration to aim for a given mutation load.
Do note that this is often off due to a variety of factors and should not be a replacement for a test library, especially for manganese mutagenesis.
If the PCR has not been done yet, expect around 1,000 ng yield for a 25 µl PCR reaction —the PCR yields with Mutazyme are generally lower than with Phusion, so if you have a value with a different polymerase underestimate from that.

Input

Mutation rate
mut/kb/div

PCR yield
ng

PCR template
ng

Size
kb


The number of doublings is xx.
The expected mutational load is xx per kb.
The expected mutational load is xx per amplicon.

PCR maths

Theoretical maximum PCR yield

Description

This is just an easy demo. It works, but it's kind of pointless as your yield will be around 50 ng per µl rxn and nowhere close to the theoretical maximum. It was made simply as a demo self standing block.

To predict how many doubling one could get it is often handy to know the theoretical maximum aDNA yield from a PCR. As is clear from a QPCR curve, a PCR does not run forever and stops after some cycles, either the primers or dNTPs are finished.
This is a rough guess for various reasons.

  • This theoretical maximum is not attainable due to minor products or PCR poisoning by various compounds (e.g. dUTP, dITP, dNDPs, magnesium pyrophosphate crystals etc.)
  • It could even be higher due to pippetting inaccuracies, spectral contaminants (e.g. isopropanol from QG buffer).
  • Not all bases are used equally...

N.B. A 20 nt primer final concentration of 2.50 ng/µl (an oddity of the Genemorph II kit) is 0.38 µM.

Input

Reaction
µL

Amplicon size
bp

Concentration
µM

Final conc. primers
µM

Conc. primers
µM

Vol. primers
µL

final µM dNTP
µM

µM dNTP
µM

µl dNTP
µL