The Perl-model manuscript (and the data) still need lots of work

I guess it's not surprising that I'd overestimated how close to completion the work is for the manuscript that, among other things, describes results from our computer simulation (Perl) model of uptake sequence evolution . As it's the only uptake sequence manuscript we still have under way, I think I'll start by giving it a simpler title. But first I'd better summarize what it now contains.

1. Analysis of the true consensus and variation in uptake sequence motifs in all the bacterial genomes that have uptake sequences (= the family Pasteurellaceae (USS) and the genus Neisseria (DUS)).
2. Analysis of variation in DUS and USS motifs across different location categories (in coding sequences, in non-coding sequences, in terminator positions).
3. Analysis of covariation between the different positions of the DUS and USS uptake sequence motifs (e.g. does having a particular base at one position correlate with having a particular base at another position).
4. Additional experimental data on how variation in uptake sequence affects uptake by H. influenzae. (This will just be a paragraph as it only modestly enriches a previously published dataset.)
5. Development of a computer-simulation model of uptake sequence evolution, and use of it to investigate the roles of key factors in maintaining uptake sequences in the non-coding parts of genomes.

In its present incarnation the manuscript is titled Evolution of DNA uptake sequences under molecular drive, but that title really only refers to the simulation model part. The real title should probably include the word 'variation', because that's what's been missing from previous work. For now, in this blog, I think I'll refer to it as the US-variation manuscript. (I reserve the right to come back and change the previous sentence if I find a better name.)