Publications - Published papers

Please find below publications of our group. Currently, we list 500 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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Memory Efficient Folding Algorithms for Circular RNA Secondary Structures

Ivo L. Hofacker, Peter F. Stadler

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Bioinformatics 22: 1172-1176 (2006)

Abstract


A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from "internal" and "external" substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only. Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of "post-processing" of the linear structures.

Keywords


RNA secondary structure, circular RNA, dynamic programming, viroids

Note


Earlier Version in: German Conference on Bioinformatics 2005, pp. 15-25; A. Torda, S. Kurtz, M. Rarey (eds.), LNI P-71 Gesellschaft f. Informatik, Bonn, 2005.