RALEE is a major mode for the Emacs text editor
(http://www.gnu.org/software/emacs/) that facilitates editing of
multiple sequence alignments of structured RNAs. Despite a range of
excellent alignment editors, few cater specifcally for this problem.
You can pick up the ELISP code for RALEE together with docs and
examples from:
http://www.sanger.ac.uk/Users/sgj/ralee/
Features include:
- colour alignments based on a consensus secondary structure, or more
conventional sequence identity measures
- employ helper applications to predict and display secondary
structures on the fly
- insert and delete columns of gaps, and shunt blocks of sequence
around at will
- 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 of Emacs means you get file handling, undo functionality and
portability for free!
This is pretty preliminary stuff, but its already proving useful to
curators of the Rfam database
(http://www.sanger.ac.uk/Software/Rfam/). Suggestions/abuse/bug
reports welcome!
Sam
