Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 03-026

[PostScript] [PDF]

Alignment of RNA Base Pairing Probability Matrices

Ivo L. Hofacker Stephan H.F. Bernhart Peter F. Stadler

Submitted to:
J.Exp.Zool. MDE

Many classes of functional RNA molecules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore be constructed only when the shared structural features are taken into account. Since multiple alignments are used as input for many subsequent methods of data analysis, structure based alignments are an indispensable necessity in RNA bioinformatics.
Results We present here a method to compute pairwise and progressive multiple alignments from the direct comparison of basepairing probability matrices. Instead of attempting to solve the folding and the alignment problem simultaneously as in the classical Sankoff algorithm we use McCaskill's approach to compute base pairing probability matrices which effectively incorporate the information on the energetics of each sequences. A novel, simplified variant of Sankoff's algorithms can then be employed to extract the maximum weight common secondary structure and an associated alignment. Availability The programs pmcomp and pmmulti described in this contribution are implemented in Perl, and are available on request from the authors. A web server is available at

Keywords: Sankoff Algorithm, RNA Secondary Structure, Structure-Based Alignments

Alternative Numbers:

Return to 2003 working papers list.
Last modified: 2003-12-19 16:55:23 studla