Publications - Published papers

Please find below publications of our group. Currently, we list 496 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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Alignment of RNA Base Pairing Probability Matrices

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

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Bioinformatics 20 (14): 2222-2227 (2004)

Abstract


<b>Motivation:</b><br/> 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.<br/> <b>Results:</b><br/> 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.<br/> <b>Availability:</b><br/> 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 <a href="http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl">http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl</a>

Keywords


Sankoff Algorithm, RNA Secondary Structure, Structure-Based Alignments