Thanks for the reply, Sam.
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On 21/07/2010 09:41, Sam Griffiths-Jones wrote:
By "annotate" do you mean mark them up in the alignment with some kind of colour scheme? It is really useful to be able to switch between different coloured markups when viewing/editing RNA alignments. I don't currently have any schemes that markup bulges and loops, but if you come up with something useful in this regard then that's great! I guess in particular that highlighting tetraloops might be useful.
Ok. Noted. Though I'm guessing that tetraloops aren't something you can simply identify with a regular expression (which would make the markup easy), we'll simply see what we (Lauren 
) can do!
Jim.
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