Folding algorithm based on nucleotide cyclic motifs. http://www.tbi.univie.ac.at/software/mcfolddp/
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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. http://www.major.iric.ca/MC-Fold/
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.
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)