https://github.com/marcom/difffoldrna.jl

Differentiable RNA partition function and sequence design
https://github.com/marcom/difffoldrna.jl

Last synced: 8 days ago
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Differentiable RNA partition function and sequence design

• Host: GitHub
• URL: https://github.com/marcom/difffoldrna.jl
• Owner: marcom
• License: mit
• Created: 2023-01-27T15:55:53.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2023-08-15T09:53:14.000Z (over 1 year ago)
• Last Synced: 2024-11-13T03:07:47.722Z (2 months ago)
• Language: Julia
• Size: 30.3 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# DiffFoldRNA.jl

[![Build Status](https://github.com/marcom/DiffFoldRNA.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/marcom/DiffFoldRNA.jl/actions/workflows/CI.yml?query=branch%3Amain)

Differentiable RNA partition function calculation for sequence

probability distributions and sequence design.  This implementation is

currently CPU-only and can only deal with smallish sequences in a

reasonable time.

There is also a [jax implementation](https://github.com/rkruegs123/jax-rnafold)

that can run on a GPU and can deal with somewhat longer sequences.

## Installation

```julia

using Pkg

pkg"add https://github.com/marcom/DiffFoldRNA.jl"

```

## Usage

```julia

using DiffFoldRNA

```

### Sequence design

```julia

target = "(((...)))"

design_ptarget(target, ViennaModel(); optim_options=(; iterations=10))

```

### Sequence-structure partition function

```julia

seqstruct_partition(ones(10,4)/4, ViennaModel(); hpmin=3)

```

## Citation

Matthies, Krueger, Torda, Ward. Differentiable Partition Function

Calculation for RNA, bioRxiv, 2023.

https://www.biorxiv.org/content/10.1101/2023.01.30.526001v2.abstract