Sam Griffiths-Jones :: RALEE
0.7 update -- 2012-03-31
Download version 0.7 below. This version has numerous bug fixes and minor feature requests. See the README file for more details.
RALEE - RNA ALignment Editor in Emacs
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 extremely immature, but has been very useful to Rfam people. 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.tar.gz -- version 0.7 (2012-03-31)
Changes in version 0.7:
- Unblock blocked alignments on loading.
- Changed behaviour for colour by base identity methods.
- New add and remove basepair methods.
Installation is pretty trivial -- view the README. While you're there, you should probably also read about bugs and caveats!
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.
Not sure why you would want these -- perhaps because you have found a new show-stopping bug (which of course you should shout loudly about).
Make "if you use it, cite it" your motto!
View my other publications.