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RNA alignment editing in Emacs -- Examples
------------------------------------------
A1. Take a look at a Stockholm format alignment file with your
favorite editor:
$ emacs examples/U12_unblocked.stk
The bottom bar of your Emacs window should contain (Ralee) or
(Ralee Protect). If it doesn't then type:
M-x ralee-mode
M-x means "hit the escape key followed by x" or "hold Alt and
press x" if your setup is vaguely normal.
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) -- Emacs may have already run
this method for you on loading. 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.
--
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
You could also invoke this method from the "Edit" menu.
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.
--
C1. Open the larger RNase P alignment (examples/RNaseP.stk).
C2. Toggle the "protect" mode ("M-x protect-mode" or use the "Edit"
menu). See how the behaviour changes by inserting and deleting
some characters.
C3. Move around the alignment with C-f, C-b, C-n, C-p and the arrow
keys.
C4. Predict the structure of a sequence in the alignment by moving the
cursor to that sequence and invoking the fold-sequence method
(shortcut C-c C-f). You must have ViennaRNA installed, and have
RNAfold in your path for this to work.
C5. Colour the alignment by the new predicted structure. Click on the
"#=GR" line and run the paint-buffer-by-current-ss-line method
(C-c C-n, or use the "Colour" menu).
C6. Flip the coloured markup between the single sequence structure
prediction and the consensus structure. Note that the 5th helix
(pink in my window!) doesn't match the consensus structure well.
Try and fix this by inserting and deleting a gap in the "SS_cons"
line. Re-colour the buffer with C-c C-b to see the effects of
your changes.
C7. Click on a base in the first helix, and hit C-c C-p
(M-x jump-to-pair). Hit C-c C-p again. Now try C-c C-o. Note
what happens if you insert or delete gap characters in one window.
C8. Finally, try inserting and deleting a few columns of gaps with C-c
C-i, and C-c C-d.
C9. Have a hunt round the "Edit", "Colour" and "Structure" menus for
other cool things to do!
--
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