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Bioinformatics Advance Access originally published online on February 1, 2006
Bioinformatics 2006 22(10):1172-1176; doi:10.1093/bioinformatics/btl023
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Memory efficient folding algorithms for circular RNA secondary structures

Ivo L. Hofacker 1,* and Peter F. Stadler 2,1,3

1 Institute for Theoretical Chemistry, University of Vienna Währingerstr. 17, A-1090 Vienna, Austria
2 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig Härtelstrasse 16-18, D-04107 Leipzig, Germany
3 The Santa Fe Institute 1399 Hyde Park Road, Santa Fe, NM, USA

*To whom correspondence should be addressed.

Background: 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.

Result: Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of ‘post-processing’ of the linear structures.

Availability: The circular folding algorithm is implemented in the current version of the of RNAfold program of the Vienna RNA Package, which can be downloaded from http://www.tbi.univie.ac.at/RNA/

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

Received on November 5, 2005; revised on December 3, 2005; accepted on January 23, 2006

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