code of the paper 'SCP4SSD: a Serverless Cloud Platform for the prediction of nucleotide Sequence Synthesis Difficulty'

DNA Synthesis Difficulty Prediction

A web-based serverless application predicts DNA synthesis difficulty of any given nucleotide sequences.

Introduction • Installation • Usage & Example • Cite us ❤

Introduction

This project is inspired from a research paper. And based on their work, we 1) explore more nucleotide sequence features (from 38 --> 426) 2) train a more powerful model (from single RF ---> ensemble learning) 3) adopt more complex feature selection methods (from random selection ---> GA, variance, correlation methods)

Installation

1. Clone the repo

git clone https://github.com/JustinDoIt/scp4ssd.git
cd scp4ssd

2. Create Anaconda Environment

conda env create -f environment.yml

3. Activate the environment

conda activate scp4ssd

4. Install auto-sklearn

conda install auto-sklearn=0.14.6 -c conda-forge

(Offical Installation)

Usage & Example

python predict.py --fasta ./examples/example.fna --out ./examples/example_out.csv

Cite us

If this repo help you, happy to cite our paper (coming soon...)

License

Distributed under the MIT License. See LICENSE for more information