February 1, 2006Bioinformatics203 citationsOpen Access
View Full PaperMemory efficient folding algorithms for circular RNA secondary structures
Structured PICO
P
Population
Circular RNA molecules (e.g., viroid genomes)
I
Intervention
Memory-efficient circular folding algorithm implemented in RNAfold
C
Comparator
Standard linear RNA structure prediction algorithms or straightforward circular structure computation requiring more memory
O
Outcome
Computation of circular secondary structures without additional memory requirements
A new memory-efficient algorithm allows for the prediction of circular RNA secondary structures without the high memory overhead of previous methods.
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 http://www.tbi.univie.ac.at/RNA/