RNA-km

February 4, 2024 ยท View on GitHub

About The Project

The implementation of the paper "Language models enable zero-shot prediction of RNA secondary structure including pseudoknots".

Getting Started

Prerequisites

Install PyTorch 1.6+, python 3.7+

Installation

  1. Clone the repo
git clone https://github.com/gongtiansu/RNA-km.git
  1. Install python packages
cd RNA-km
pip install -r requirements.txt
  1. Download pretrained model weight and place the pth file into the weight folder
mkdir weight
mv weight.pth weight

Usage

  1. RNA-km.py: extract RNA sequence representation (L * 1024) and attention maps from sequence (fasta format)
python RNA-km.py -i <RNA_fasta> -o <output_dictionary> (--attn) (--cuda)

Example

cd example
./run_example.sh

License

Distributed under the MIT License. See LICENSE for more information.