I am trying to mimic the visual output of BLAT output from the UCSC BLAT server. Specifically, I want to see black bars, with letter highlighting variations in the sequence (what one would see after clicking on "browser" in the BLAT output window.) I am trying to run BLAT locally, to get past the 25 sequence limitation. I have searched the mailing list, and have tried the pslPretty -axt | axtToMaf scripts, but do not get the same black bar output with the differing bases being the only visible bases. I feel that I might be misunderstanding the final modification needed in the maf file itself. Can you go through the process in a bit more detail? Thanks! Jamie
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