PMcomp / PMmulti

Structural Alignment of RNA

pmcomp and pmmulti are two programs to perfrom pairwise and progressive multiple alignments of RNA sequences. pmcomp is a variant of Sankoff's algorithm for simultaneous folding and alignment, which takes as input pre-computed base pair probability matrices from McCaskill's algorithm as produced by RNAfold -p. Thus the method can also be viewed as way to compare base pair probability matrices.
pmmulti is a simple wrapper program that does progressive multiple alignments by repeatedly calling pmcomp

At the moment we offer prototypes for the programs written in Perl. A faster C version will hopefully follow soon.
Use the following links to download the (updated 11/9/04) and scripts.

Run --man or --man to view the respective man pages.

For more information see:
Ivo L. Hofacker, Stephan H.F. Bernhart, Peter F. Stadler
Alignment of RNA Base Pairing Probability Matrices
Bioinformatics 20: 2222-2227 (2004)

The following files contain input data for the examples shown in the paper:

Ivo Hofacker <>

Last modified: 2004-11-09 18:00:39 ivo