RALEE — RNA ALignment Editor in Emacs

0.8 update — 2014-11-16

Download version 0.8 below. This version has a few important bug fixes, and cleaner errors and messages. See the README file for more details.

What is this?

RALEE is a major mode for the Emacs text editor. It provides functionality to aid the viewing and editing of multiple sequence alignments of structured RNAs. It is hacky and buggy, but has been very useful to SGJlab people, Rfam people, and even a few others. Features include:

  • colour bases in alignment according to:
    • secondary structure
    • base conservation
    • base identity
  • insert and delete columns of gaps
  • protect the alignment from inadvertent insertion of junk and deletion of important things
  • split the screen to edit open and closing regions of a helix together
  • use helper applications to view secondary structures, and use the colour markup to see how well the sequences fit these structures
  • write a postscript file of the alignment including colourful markup

Download ralee-mode-0.8.tar.gz — version 0.8 (2014-11-16)

Changes in version 0.8:

  • Unblock alignment function now deals with #=GR lines.
  • Tabs are dealt with sensibly by converting to spaces.
  • Postscript writing function has been cleaned up.
  • There are some more sensible error and status messages.
  • RALEE will check automatically for updates without calling external perl code.

Installation is pretty trivial — view the README. While you’re there, you should probably also read about bugs and caveats.

What does it look like?

u1

Using RALEE mode in GNU Emacs to edit an alignment of some U1 spliceosomal RNA sequences. The secondary structure base pairing pattern is annotated as nested pairs of < and > symbols. Bases of the same colour are part of the same helix. The split-screen view allows editing of base paired regions of the alignment even if they are far apart in sequence. For instance, the yellow bases in the top panel pair with the yellow bases in the bottom panel.

How do I download it?

Not sure why you would want anything but the latest version — perhaps because you have found a new show-stopping bug (which of course you should shout loudly about).

How do I cite it?

[See our Complete publication list]