KirolosMagdyGirgs/CGR-ICGR

CGR(Chaos game representation) is visualization of genetic materials ( DNA or Protein sequences) using the concept of Chaos graphical representation for easier and faster analysis. ICGR(Integer Chaos game representation) is adding the feature of encoding of DNA sequence into 3 integers that can be decoded back to the original sequence

Python

CGR - ICGR

(CGR)Chaos-game-representation-of-genetic-materials

Visualization of genetic materials ( DNA or Protein sequences) using the concept of Chaos graphical representation for easier and faster analysis

(Example of the output)

(ICGR)Integer chaos game representation :

based on https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0173?journalCo
Encoding DNA sequences into 3 integers ( the first and the second integer represent the X and Y coordinates and the third number represents the length of the sequence ) that can be decoded back into the original sequence
we added the ability to encode sequences longer than 1024 nucleotides

(Example of the output )

Table of Contents:

GUi (folder contatining the files of the front-end of the website (code in HTML and CSS and screenshots) )
Test samples ( fastA and fastQ files used to test the code)
Video (a description video of the concept of the project )
Project proposal (containing more info about the project)
CGR.py ( the code of the cgr )
ICGR.py ( the code of the icgr )

How to run :

python 3.8 is needed !!

download the python file (.py) and run using python environment

contributors :

Kirolos Magdy
Mohammed Nasef
Sara Hammad
Samia Elrefaey
Asmaa Ayman
Jihad Shehata
Reham El-Baz

this project is made under the observation of Dr/ Sara El-Metwally - the faculty of computer science Mansoura University

References:

https://towardsdatascience.com/chaos-game-representation-of-a-genetic-sequence-4681f1a67e14

https://www.youtube.com/watch?v=oaG7ocRs5Ek

https://www.youtube.com/watch?v=IGlGvSXkRGI&list=WL&index=161

https://github.com/cyinbox/iCGR