Well, I don't know why my first attempt at running a Gibbs motif search with the Gallibacterium genome returned errors. The errors it described were ones I hadn't made (as far as I could tell), so I resubmitted the runs and they were fine.
But the grid-computer system was slow to get around to my runs (probably those physicists and meteorologists hogging the system), so I poked around and rediscovered that the Gibbs motif searcher program now also runs on Macs. Luckily one of the post-docs had just come back from a two-week course that required intensive use of Unix, so she was able to dive in and sort out the permissions etc. for me. So now I can run the Gibbs searches on my newish MacBook Pro and on our other fast Mac. And I can also still run them on the grid system too.
Results: I can't find anything (i.e. Gibbs can't find anything) in the Gallibacterium genome that looks anything like a typical Pasteurellacean uptake sequence. I've done simple searches where I just asked it to look for an 8-mer motif, and searches wherre I gave it 'segmentation-mask' prior files telling it the spacing typical of a H. influenzae or A. pleuropneumoniae USS, but it still didn't find anything. Most of the time it can't find anything it even considers to be a motif at all. This may be because the USS motifs are too sparse for it to pick them up, or because Gallibacterium really doesn't have a USS at all.
But I'm trying one more thing - giving it a prior file that specifies not just the spacing but the actual position weight matrix to expect. If this doesn't find anything we may need to do some uptake-specificity experiments.
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Not your typical science blog, but an 'open science' research blog. Watch me fumbling my way towards understanding how and why bacteria take up DNA, and getting distracted by other cool questions.
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