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Bioinformatics Advance Access published online on September 17, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth489
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 1, 2004
Revised August 16, 2004
Accepted August 17, 2004

Applications note

RALEE - RNA alignment editor in Emacs

Sam Griffiths-Jones 1*

1 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CAMBS, CB10 1SA, UK

* To whom correspondence should be addressed. E-mail: sgj{at}sanger.ac.uk.


  Abstract

Summary: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilising helper applications for structure prediction, and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS.

Availability: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples.


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