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https://github.com/marcom/foldrna.jl
Nucleic acid secondary structure prediction and analysis
https://github.com/marcom/foldrna.jl
julia rna rna-folding rna-secondary-structure rna-secondary-structure-prediction
Last synced: 3 months ago
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Nucleic acid secondary structure prediction and analysis
- Host: GitHub
- URL: https://github.com/marcom/foldrna.jl
- Owner: marcom
- License: mit
- Created: 2021-11-22T19:06:20.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-01-17T19:14:41.000Z (12 months ago)
- Last Synced: 2024-09-18T12:07:09.945Z (4 months ago)
- Topics: julia, rna, rna-folding, rna-secondary-structure, rna-secondary-structure-prediction
- Language: Julia
- Homepage:
- Size: 115 KB
- Stars: 5
- Watchers: 3
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# FoldRNA
[](https://github.com/marcom/FoldRNA.jl/actions/workflows/CI.yml?query=branch%3Amain)
This is an implementation of nucleic acid secondary structure
prediction and analysis algorithms in Julia.
## Installation
Press `]` in the Julia REPL to enter package mode and enter
```
add FoldRNA
```
## Basic usage
```julia
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, "(((...)))")
```
## Related Julia packages for RNA secondary structure
- [Infernal.jl](https://github.com/cossio/Infernal.jl)
- [LinearFold.jl](https://github.com/marcom/LinearFold.jl)
- [PlotRNA.jl](https://github.com/marcom/PlotRNA.jl)
- [Rfam.jl](https://github.com/cossio/Rfam.jl)
- [RNAstructure.jl](https://github.com/marcom/RNAstructure.jl)
- [ViennaRNA.jl](https://github.com/marcom/ViennaRNA.jl)