Missing functionality from ViennaRNA - Githubissues

marcom / ViennaRNA.jl

Julia interface to ViennaRNA for RNA structure prediction and analysis

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Missing functionality from ViennaRNA #14

Open marcom opened 1 year ago

marcom commented 1 year ago

Some of these items might already work, but should still get their own testset in the tests/ dir.

ViennaRNA-2.5.0 and before

default temperature for DNA params is 37 °C (like for RNA), change to better default

Callback functions

[ ] subopt
[ ] pbacktrack
[ ] neighbours
more?

Windowed predictions

See also: https://github.com/marcom/ViennaRNA.jl/issues/9

[ ] pf_window
[ ] pf_window_channel
[ ] bpp_window (using vrna_probs_window)
[ ] bpp_window_channel
zscore

Soft and hard constraints

[ ] soft constraints
[ ] hard constraints

G-quadruplexes

Duplex predictions

strand concentrations?

Multistrand predictions

strand concentrations

RNA-DNA hybrids

only duplexes?

Grammar callbacks

callbacks at various stages of recursions

ViennaRNA-2.6.0

https://github.com/ViennaRNA/ViennaRNA/releases/tag/v2.6.0

energies for modified bases (uses soft constraints callback), energy parameter modifications stored as json
adjust energies to different salt concentrations (Na+)
new soft constraints multi-callback dispatcher