DOI: 10.5281/zenodo.11111708
title: Frequency chaos game method and fractals show evolutionary relationships of the PRKN gene in primates

description: Supplementary Material:

01 Supplementary Material: Contains an Excel file named “Frequency and relative frequency of nucleotides in primate PRKN” with the nucleotide relative and total frequency for each species. Moreover, the individual nucleotide relative and total frequency are represented in bar charts graphics and are located in two separated subfolders named “01 PRKN nucleotide relative frequency” and “02 PRKN nucleotide total frequency” respectively, with the name of each species. 

02 Supplementary Material: Contains the graphic representation of the fractals generated for the 16 PRKN sequences of primates. The graphics are located in 16 subfolders labeled with each primate scientific name. Each one contains 9 images that corresponded to k-mers from 3 to 11, and were generated by the "Frequency Chaos Game Representation" methodology. These were titled with the name of the species, the letter “k” and the corresponding number of "K-mers". Likewise, the order of the quadrants to form the fractal was: Upper, Guanine – Thymine and Lower, Cytosine – Adenine.

03 Supplementary Material: Contains the information obtained to fractals constructed with 7-mers, divided in three subfolders:





01 K-mer nucleotide appearance frequency and composition: contains 16 folders with the name of each species. The folders contain two files: a graphic representation of the 7-mers frequency in a .png format and a .txt file with the detailed 7-mers nucleotide content. 




02 Fractal_7-mer: contains 16 .png files with the graphic representation of the fractals generated for each PRKN gene primates sequences, with the quadrants arrangement proposed in the methodology: upper, Cytosine-Adenine; lower, Thymine-Guanine; and the "Frequency Chaos Game Representation" methodology. The graphics are labeled with the species name.




 03 Landscape 3D fractal: contains 16 .png files with the graphical representation of landscape 3D fractals constructed with the 7-mers. The graphics are labeled with the name of the primates species.



04 Supplementary Material: Contains 16 .png files that correspond to the fractals images generated with the Chaos Game Representation (CGR) algorithm, for the primates PRKN gene sequences, with 7-mers to corroborate the fractals generated with the FCGR methodology and the quadrants arrangement proposed. The files are labeled with the name of the species. 

05 Supplementary Material: Contains two files: a .png named “Entropy_primate_species” that corresponds to the graphical representation of the primates species’ Shannon entropy; and an Excel file named “Shannon_entropy_Primate_species” that corresponds to a table with the individual Shannon entropy for the primates species.

06 Supplementary Material: Contains two .png files labeled “Dendrogram_Cophenetic_horizontal.png” and "Dendogram_7-mers_out.png" that correspond to the dendrograms constructed to PRKN gene, with a size of 7-mers, without and with the outgroup respectively. 
description: This work was supported by Maestria en Ciencas de la Complejidad from the Universidad Autonoma de la Ciudad de Mexico, Campus Colonia del Valle, Mexico; by the Complexity Science Group: Chaos, Fractals, Nature Applications from the Universidad Autonoma de la Ciudad de Mexico. Moreover, by a research stay granted by the Universidad Industrial de Santander by resolution 558 of October 20, 2023, and for the Grupo de Investigación en Computo Avanzado y a Gran Escala (CAGE) from Centro de Supercomputacion y Calculo Cientifico of the Universidad Industrial de Santander.