Sam Griffiths-Jones :: RALEE
0.61 update -- 2007-12-06
Download version 0.61 below. This fixes a bug in version 0.6 with gap positions in structure lines predicted with fold-structure. Aliternatively, you can just download the replacement ralee-helpers.el file, and overwrite the corresponding file from release 0.6.
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 is already proving 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 0.61 (2007-12-06)
Changes in version 0.6x:
- protect-mode is now off by default.
- Compensatory changes markup scheme is changed.
- Realign defined blocks of the alignment using clustalw.
- Sort sequences by id and tree.
- Fetch and view sequence annotation from NCBI entrez.
Installation is pretty trivial -- view the README. While you're there, you should probably also read about bugs and caveats!
Screenshot
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.
Old versions
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).
- ralee-mode-0.6 (2007-12-04)
- ralee-mode-0.5 (2005-07-10)
- ralee-mode-0.4 (2004-09-23)
- ralee-mode-0.3 (2004-06-30)
- ralee-mode-0.2 (2004-06-08)
- ralee-mode-0.1 (2004-05-31)
Sam Griffiths-Jones