RNA alignment editing in Emacs -- Examples
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A1. Take a look at a Stockholm format alignment file with your
    favorite editor:

	 $ emacs examples/U12_unblocked.stk

    Note the format of the SS_cons line that describes the secondary
    structure of RNA.


A2. Try out the paint-buffer-by-ss method by hitting Ctrl-c Ctrl-b
    (henceforth abbreviated C-c C-b).  You should see that helices
    appear in different colours.  Bases that don't pair in
    Watson-Crick fashion (or G=U) are not coloured.  You should see an
    uncoloured A-C pair in the second helix.

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B1. Open the blocked version of the U12 alignment:

	 $ emacs examples/U12_blocked.stk

B2. Convert the alignment to an unblocked format using:

	 M-x unblock-alignment

    M-x means "hit the escape key followed by x" or "hold Alt and
    press x" if your setup is vaguely normal.

B3. Verify that you can colour the buffer according to the secondary
    structure markup.

B4. Try the paint-buffer-by-cons method by hitting C-c C-c.  Columns
    are coloured according to base conservation.

B5. Try the paint-buffer-by-base method by hitting C-c C-v.  Columns
    are coloured according to base identity.

B6. Have a look round the "Colour" menu to remind yourself of the
    colouring options.

B7. Save the unblocked version to a new file with C-x C-s.

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