The algorithm implemented here-in provides extended RNA
secondary structure prediction. Each predicted nucleotide
pairing is extended with an annotation describing which of
three nucleotide edges is engaged in the pairing. In addition,
each nucleotide may be engaged in more than one pairing.
The algorithm is 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
http://www.tbi.univie.ac.at/software/rnawolf/
Please note that "experimental" does mean experimental. We are
mostly concerned with determining a good set of (heuristic)
rules for run-time reduction currently. This version does
include stacking and is able to fold sequences of a few hundred
nucleotides in seconds.
Triplet calculations will come back with the next version (in a
few days). The recursions require a number of changes to keep
the runtimes down (as has been done for the extended loops
without triplets).
We have recently split the Biohaskell libraries into smaller
individual libraries. In addition, stacking, intermediate
arrays, fusion and newtype-wrapping did require a number of
changes. Please send a mail, if you encounter strange behaviour
or bugs.
Changes in 0.4.0.0
Changes in 0.3.2.0
Changes in 0.3.1.0
