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Bioinformatics Advance Access originally published online on April 8, 2004
Bioinformatics 2004 20(14):2222-2227; doi:10.1093/bioinformatics/bth229
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Bioinformatics 20(14) © Oxford University Press 2004; all rights reserved.

Alignment of RNA base pairing probability matrices

Ivo L. Hofacker *, Stephan H. F. Bernhart and Peter F. Stadler

Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstrasse 17, Vienna, A-1090, Austria and Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstrasse 7b, Leipzig D-04103, Germany

Received on December 14, 2003; accepted on February 3, 2004
Advance Access Publication April 8, 2004

Motivation: 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 base pairing probability matrices. Instead of attempting to solve the folding and the alignment problem simultaneously as in the classical Sankoff's 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 can be downloaded together with the example datasets from http://www.tbi.univie.ac.at/RNA/PMcomp/. A web server is available at http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl

Contact: ivo{at}tbi.univie.ac.at

* To whom correspondence should be addressed.


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