Defining the uptake signal sequence

The big goal for today is to make progress on the manuscript where we pin down the specifics of the Haemophilus influenzae 'uptake signal sequence' (USS). This DNA sequence can be defined in two ways, both as the sequence motif preferentially taken up by competent H. influenzae cells, and as a sequence motif that's strikingly overabundant in the H. influenzae genome. The two are of course related; we think that the abundance on the genome is a direct consequence of preferential uptake and random (unbiased) recombination between incoming DNA and the chromosome.

The most glaring hole in the manuscript right now is the Methods section where I need to describe the bioinformatics methods I've used to analyze the USS motif in the genome. The post-doc responsible for the DNA uptake experiments has already written her part of the Methods, and today we're going to sit down together and write my part, as well as work on polishing the Results (I think this is in OK shape) and the Discussion (needs work!).