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
Program
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 pmcomp.pl (updated 11/9/04) and
pmmulti.pl
scripts.
Manual
Run pmcomp.pl --man or pmmulti.pl --man to view
the respective man pages.
Literature
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)
Examples
The following files contain input data for the examples shown in the
paper:
Ivo Hofacker <ivo@tbi.univie.ac.at>
Last modified: 2004-11-09 18:00:39 ivo