Publications - Published papers

Please find below publications of our group. Currently, we list 508 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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Partition Function and Base Pairing Probabilities for RNA-RNA Interaction Prediction

Fenix W. D. Huang, Jin Qin, Christian M. Reidys, Peter F. Stadler

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Bioinformatics 25:2646-2654 (2009)

Abstract


The RNA-RNA interaction problems (RIP) deals with the energetically optimal structure of two RNA molecules that bind to each other. The standard model introduced by Alkan <em>et al.</em> (J. Comput. Biol. <b>13</b>: 267-282, 2006) allows secondary structures in both partners as well as additional base-pairs between the two RNAs subjects to certain restrictions that allow a polynomial-time dynamic programming solution. We derive the partition function for RIP based on a notion of "tight structures" as an alternative to the approach of Chitsaz <em>et al.</em> (Bioinformatics, ISMB 2009). This dynamic programming approach is extended here by a full-fledged computation of the base-pairing probabilities. The <i>O(N<sup>6</sup>)</i> time and <i>O(N<sup>4</sup>)</i> space algorithm is implemented in C (available from <tt>http://www.combinatorics.cn/cbpc/rip.html</tt>) and is efficient enough to investigate for instance the interactions of small bacterial RNAs and their target mRNAs.

Keywords


RNA-RNA interaction, joint structure, dynamic programming, partition function, base pairing probability, loop, RNA secondary structure.