Folding algorithm based on nucleotide cyclic motifs.

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GPL-3 licensed by Christian Hoener zu Siederdissen, Stephan H Bernhart, Peter F Stadler, Ivo L Hofacker

This is a RNA secondary structure prediction tool based on the idea of combining small motifs, called nucleotide cyclic motifs (NCMs). The algorithm implemented here and described in

Hoener zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL,

"A Folding Algorithm for Extended RNA Secondary Structures",

Bioinformatics (2011) 27 (13), i129-136

has polynomial runtime in O(n^3) and uses a (pseudo-energy) scoring scheme based on

Parisien M, Major F.

"The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data",

Nature 2008, 452(7183):51-55.

This program uses the same database as MC-Fold (which has exponential run-time) and aims to be able to produce the same results.

The underlying grammar of our implementation is unambiguous and allows the complete evaluation of all structures within an energy band above the ground state, presenting each unique structure just once. Alternatively, the grammar allows partition function calculations.

Current status:

  • comparable prediction accuracy on sequences (compared with MC-Fold)

  • possibility to use sparse data correction

  • handles non-ACGU nucleotides gracefully

  • suboptimals: return all structures within an energy band above the ground state

  • constraint folding (fill partial structures)


  • Boltzmann likelihood calculations

  • pseudoknot calculations (currently aiming for a pknotsRG-like algorithm)

Depends on 7 packages:
Used by 1 package:
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