This is an implementation of nucleic acid secondary structure prediction and analysis algorithms in Julia.
Press ] in the Julia REPL to enter package mode and enter
add FoldRNA
using FoldRNA
# Nussinov-Jacobson model (basepair model)
f = Fold("GGGAAACCC", RNA_BPMODEL)
mfe(f)
partfn(f)
bpp(f)
energy(f, "(((...)))")
prob_of_struct(f, "(((...)))")
# Nearest-neighbour energy model (loop model)
#
# Note: there are still some errors in the implementation of the
# energy calculation in the loop decomposition, so mfe() and
# partfn() give wrong results, but energy() should work
f = Fold("GGGAAACCC") # defaults to RNA_TURNER2004 energy params
mfe(f)
partfn(f)
# bpp(f) not implemented yet for loopmodel
prob_of_struct(f, "(((...)))")