Genmus: a Genetic Music Player

Oliver Bonham-Carter, Allegheny College

email: obonhamcarter@allegheny.edu

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Genetic Music: Use your ears to study DNA!!

Table of Contents

• Description
• Running the code
• Command Summary
• Mechanism
• Future Work

Description

DNA to Piano Music Converter: Put DNA sequences into piano from PubMed FASTA files.

Running the code

You must first install Poetry to manage the code's dependencies, and to run the program.

 [--bighelp] This page, right?
 [--opt S] Create a music scale
 [--opt T] Create song: Twinkle-Twinkle Little Star
 [--opt H] Create song: Happy Birthday
 [--data ./data --file file.fasta] Load fasta file, convert dna to score
 Setup with Poetry :  poetry install

 😀 USAGE: poetry run genmus --dir ./data/ --file mydata.fasta 

Command Summary

• To prepare and play a basic scale
  • poetry run genmus --opt s
• To prepare and play Twinkle-Twinkle little star
  • poetry run genmus --opt T
• To prepare and play Happy Birthday (sort of)
  • poetry run genmus --opt H
• To prepare and play some genetic music from a DNA in fasta data file (mydata.fasta) which is located in ./data/
  • poetry run genmus --dir ./data/ --file mydata.fasta

OUTPUT: All output wav files are saved in the directory `0_out/

Mechanism

How does Music Come From DNA Sequence?!

As you may know, protein is synthesized from amino acids. Each amino acid is encoded by three adjacent DNA bases (called "condons" or "triplets") from a sequence of DNA (a gene). GenMus works by pretending to synthesize proteins, only not by creating protein product, but by making music. Instead of a sliding window that reads in three bases at a time to determine the placement of an amino acid, the three bases are actually converted to musical notes.

The conversion begins as a list of words of three bases which are taken from the DNA sequence. For each particular word which is encountered in the DNA sequence, a frequency is recorded. The words having the most frequent occurrence are labeled as the "common" words from a sequence. For example, the DNA sequence ATC-ATC-AAA has two occurrences of ATC and one of AAA with this given reading frame.

In a musical score, there are also common notes that you may hear. For example, in "Twinkle Twinkle Little Star" there are a good number of notes that are heard far more than others. GenMus knows the common notes of this child's song and then pairs the commonly encountered condons from a sequence of DNA with the common musical notes. The sound that you hear from the program has been generated by sliding window (moving in step three) of a DNA sequence to recognize codons and play a note that conforms to its frequency, in conjunction with that of frequency of notes of the song.

Data

The inputs for this program are DNA sequences as fasta files. These sequences can be obtained from GenBank files using the using the GetCodingSeqs (GCS) tool by the same author. GCS produces fasta files containing coding and non-coding sequences as outlined in GenBank records. All these sequences can then be fed into GenMus, or seemingly any tool that inputs fasta files. Lucky for you that this data can be created so easily, right?!

Future Work

This is a program to convert DNA sequences to piano music. The documentation for this project is coming soon to help users to use and enjoy this project. In the meantime, there is online help in the Python code to help the user to run the program.