Yesterday I worked out a way to nudge the Gibbs motif sampler into finding the Neisseria meningitidis DUS (their term for their uptake signal sequence). Even though the DUS is present in Neisserial genomes even more frequently than the H. influenzae USS is in its genome, the sampler couldn't find it without prompting. This may be because it's much shorter than the USS (only 12 contiguous bp vs 22 bp spread over 29 positions), or for some other reason I don't understand.
I didn't want to give the sampler a prior file specifying the pattern to look for, so instead I added two lines of fake sequence with a very high frequency of the DUS to the start of the genome file. This 'seed' was enough to get the sampler started on the right motif. Once it's started it has no trouble finding the DUS, and I can later delete the seeded DUSs from the list it generates.
This morning I obtained the A. pleuropneumoniae genome sequence my collaborators have been working with, split it into pieces, and generated reverse complements of both it and the N. meningitidis genome, and combined each genome's forward and reverse-complement sequences into single 'F+RC' files for searching. I did this because I need to have the sampler search both strands, and (I think) I have better control if I tell it to search just the sequence I've given it. The A. pleuropneumoniae USS is very similar to but even longer than the H. influenzae USS, so I did test runs with the 'prior' masking file I'd used for H. influenzae to make sure everything worked.
I did this and all my other tests using only 10% of the genome and only one orientation, because I wanted them to run very fast and because the guys who manage the computer cluster want all long runs to be entered through their 'Fair Share' queueing system. And now I've successfully queue'd requests for full-genome searches. I don't expect to get the results until tonight or tomorrow.
I also emailed my collaborators to let them know I'm finally back working on this project. The PI is on vacation, but the bioinformatician has been taking advantage of his absence to work full time on it! She's going to send me her new data and rewrite in a few days, so I'm not going to do any work on the manuscript until then. I could go ahead and do Gibbs analysis of all the genomes we might want to consider, but I think I should wait to see how the three main foci of our work (H. influenzae, A. pleuropneumoniae and N. meningitidis) fit into the manuscript.
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