In addition to using our uptake simulation to generate surrogate data for uptake of chromosomal fragments, I think I can also use it to generate surrogate data for the uptake experiments that start with degenerate pools based on perfect uptake sequences. In these experiments we'll generate a pool of synthetic DNA fragments (~70 bp in the latest plan, I think, although our CIHR proposal says 200 bp) with a 30 bp internal USS that is 12% degenerate at each position (maybe it's degenerate throughout its length. We plan to reisolate fragments from this pool that cells have taken up, sequence these, and analyze the patterns of variation.
I can give the uptake simulation a 'genome' consisting of just this fragment sequence, and instruct it to take up fragments of this full length (so every fragment will start out the same). I can then set the fragment-specific mutation rate to 12%, so that each fragment will be independently mutagenized to this level before being scored for possible uptake. I can test the effects of different uptake biases by using different matrices for the scoring, and different ways of using the matrices (additive, multiplicative). (I'll also ask my mathematical colleagues if there is any function that gives effects intermediate between additive and multiplicative.) If our proposed fragment is degenerate only in its USS, I'll use a USS-length fragment; if it's degenerate throughout I'll use the full length sequence.
Then I'll give the pool of simulated-uptake sequences (and a control pool of degenerate but unselected sequences) to the post-doc for analysis. He's already done a very nice preliminary analysis of the simulated chromosomal fragments.
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