Memory efficient folding algorithms for circular RNA secondary structures
Open Access
- 1 February 2006
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 22 (10) , 1172-1176
- https://doi.org/10.1093/bioinformatics/btl023
Abstract
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 Author Webpage Contact:ivo@tbi.univie.ac.atKeywords
This publication has 28 references indexed in Scilit:
- Viroids: petite RNA pathogens with distinguished talentsTrends in Plant Science, 2004
- Features Affecting the Ability of Hepatitis Delta Virus RNAs To Initiate RNA-Directed RNA SynthesisJournal of Virology, 2004
- Viroids: the minimal non‐coding RNAs with autonomous replicationPublished by Wiley ,2004
- The ability to form full-length intron RNA circles is a general property of nuclear group I intronsRNA, 2003
- Two reactions of Haloferax volcanii RNA splicing enzymes: Joining of exons and circularization of intronsRNA, 2003
- Secondary Structure Prediction for Aligned RNA SequencesJournal of Molecular Biology, 2002
- Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureJournal of Molecular Biology, 1999
- Dynamic programming alignment of sequences representing cyclic patternsPublished by Institute of Electrical and Electronics Engineers (IEEE) ,1993
- On a cyclic string-to-string correction problemInformation Processing Letters, 1990
- The equilibrium partition function and base pair binding probabilities for RNA secondary structureBiopolymers, 1990