The return of the rings

The return of the rings: Evolutionary convergence of aromatic residues in the intrinsically disordered regions of RNA-binding proteins for liquid–liquid phase separation

Dependencies

Usage

Clone and build environment

Clone this repository

git clone https://github.com/allmwh/the_return_of_the_rings.git

Build environment
```
pip install -r requirements.txt
```

After that, just type jupyter-notebook in folder, and you can run all of the code

jupyter-notebook

PONDR order/disorder identification

pondr_disorder_ident.ipynb

Get order/disorder identification infos by PONDR

Get taxonomy sequence from OMA

get_taxonomy_sequence.ipynb

The script does following steps:

Get paralogs from OMA by uniprot id, downloaded sequences are in ./output/fasta/a_oma
Group paralogs by taxonomy id, outputs: ./output/fasta/b_grouped/TAXONOMY_ID
Align sequences by Clustal Omega, outputs: ./output/fasta/c_alied/TAXONOMY_ID
Filter sequences, outputs: ./output/fasta/d_extre_filtered/TAXONOMY_ID

Generate data and figures

fig1a.ipynb
fig1b.ipynb
fig2.ipynb

Following scripts instructions to generate data and figures

Citation

@article{https://doi.org/10.1002/pro.4317,
author = {Ho, Wen-Lin and Huang, Jie-rong},
title = {The return of the rings: Evolutionary convergence of aromatic residues in the intrinsically disordered regions of RNA-binding proteins for liquid–liquid phase separation},
journal = {Protein Science},
doi = {https://doi.org/10.1002/pro.4317},
year = {2022}
}