RNA Structure and Sequence alignment

NEW: Foldalign version 2.1.1 is now available. Get the software here.
NEW: FoldalignM version 1.0.1 is now available. Get the software here.
The FOLDALIGN web server 2.1.0.A is available here.

The new Semi-Automated RNA Sequence Editor SARSE might also be of interest.

FOLDALIGN an algorithm for local or global simultaneous folding and aligning two or more RNA sequences and is based on the Sankoffs algorithm (SIAM J. Appl. Math., 45:810-825, 1985). Foldalign can make pairwise local or global alignments and structure predictions. FoldalignM makes a multiple global alignment and structure prediction.

Recent references

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix,
Havgaard JH, Torarinsson E, Gorodkin J. PLOS computational biology. 3:e193, 2007

Multiple structural alignment and clustering of RNA sequences,
Torarinsson E, Havgaard JH, Gorodkin J. Bioinformatics. 23:926-32, 2007.

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search,
J. H. Havgaard, R. B. Lyngsø, and J. Gorodkin. Nucleic Acids Research 33:W650-W653, 2005.