released on 8th Apr, 2008

Rfold HP : http://www.ncrna.org/software/rfold

Base pairing probability matrices have been frequently used for the analyses of structural RNA sequences.
Recently, there has been a growing need for computing these probabilities for long DNA sequences by constraining the maximal span of base pairs to a limited value in order to investigate a vast number of non-protein-coding RNA transcripts in eukaryotic cells.
Rfold is the first software tool that exactly computes the base pairing probabilities associated with the energy model under the constraint on the maximal span W of base pairs.
Rfold computes local base pairing probabilities for a DNA sequence of length N with time and memory complexities O(NW²) and O(N¡ÜW²), respectively.