Repository associated with the research paper on the hierarchical and nested structures in amino acid sequences.
This repository contains codes and data associated with the paper "Evolutionary Tinkering Enriches the Hierarchical and Nested Structures in Amino Acid Sequences, 2023" by Zecheng Zhang et al. This repository serves as a supplement, providing the necessary tools (also useful tools for you to calculate the ladderpath of sequences) and datasets to understand and replicate our findings.
The folder Data: Contains all the data generated and other associated scripts:
six_proteome_output_fig6a.txt: It records the ladderpath-associated indicators for every protein shown in Fig. 6 of the main text.
cal_Rk.py: Script to calculate $R_k$, which was used in Fig. 3 of the main text.
The folder LadderpathCalculator: Contains scripts and data for calculating the ladderpath, including:
README.md: Instructions on how to use the ladderpath calculation tool.
ladderpath.py: Main script for ladderpath calculation.
ladderpath_data_omega0: The folder containing supporting data for ladderpath.py. Do not modify.
The folder LadderpathCalculator-InclOrigData: Normally, you do not need this folder.
This folder is intended for developers who wish to contribute to calculating $\omega_0$ for large $S$. This folder contains the same files as the LadderpathCalculator folder. Additionally, within ladderpath_data_omega0/nBase2/ (ladderpath_data_omega0/nBase4/, ladderpath_data_omega0/nBase10/, etc.), there is a folder named OriginalData which describes how the corresponding .csv file (namely, $\omega_0(S)$) was calculated.
For a quick start on how to use the ladderpath calculation tool, navigate to the LadderpathCalculator folder and see the provided README for more detailed usage and options. Quick example:
import ladderpath
strs = ['CUCGACGACUAUCUCGACAAUGACU']
strsLP = ladderpath.ladderpath(strs, CalPOM=True)
strsLP.dispPOM()
# example output: { G, A(3), C(3), U(3) // AU, GAC // CUCGAC, GACU}
strsLP.disp3index()
# example output: ( Ladderpath-index:14, Order-index:11, Size-index:25 )