My goal of using the Gibbs motif sampler to examine the consensus of USS repeats in other genomes is getting closer.
This morning I found the Perl script we wrote to chop genomes into sub-segments for Gibbs analysis, figured out its requirements, and used it to prepare a Neisseria genome sequence for analysis. I worked out where I needed to put the resulting genome file in my directory on the computer cluster server, and used Fugu to do it. I found the instructions on how to log on to the cluster from the Mac Terminal, found my password, and figured out how to change to the directory with the Gibbs program in it. I worked out how to modify the command line to work for this genome, and YES! it worked.
Unfortunately it didn't readily find the Neisseria USS motif, even though it's a much simpler motif than the H. influenzae one, and a bit more frequent too. I'm hoping that by tomorrow my brain will have remembered how I solved this problem for H. influenzae.
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