back to the uptake-sequence variation project

Last night I reread what I've written so far on the manuscript about variation of uptake sequences.  It's a bit of a mess, because the different parts were intended for different manuscripts.  I got discouraged by all the work that still needs to be done, but this morning I'm more optimistic.  

One big job is to finish up all the analyses based on Gibbs motif searches.  I need to do the basic searches on the H. parasuis genome, do several analyses of subsets of the N. meningitidis genome, and repeat analyses of the H. influenzae genome that were originally done with a different dataset than the one I'm now using.

A second big job is to do more simulations with the Perl model of uptake sequence evolution, to give a clear picture of how a few basic factors affect their accumulation.  Right now I don't even remember which factors this should address, but I think everything is clearly set out in earlier posts and in the documents the former post-doc left me.

And the final big job is to weave the different parts together to make a manuscript that tells a coherent story.