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---
-title: Encoding binary data into DNA sequence
-permalink: /encoding-binary-data-into-dna-sequence.html
-date: 2019-01-03T12:00:00+02:00
-layout: post
-type: post
-draft: false
---
-## Initial thoughts
-Imagine a world where you could go outside and take a leaf from a tree and put
-it through your personal DNA sequencer and get data like music, videos or
-computer programs from it. Well, this is all possible now. It was not done on a
-large scale because it is quite expensive to create DNA strands but it's
-possible.
-Encoding data into DNA sequence is relatively simple process once you understand
-the relationship between binary data and nucleotides and scientists have been
-making large leaps in this field in order to provide viable long-term storage
-solution for our data that would potentially survive our specie if case of
-global disaster. We could imprint all the world's knowledge into plants and
-ensure the survival of our knowledge.
-More optimistic usage for this technology would be easier storage of ever
-growing data we produce every day. Once machines for sequencing DNA become fast
-enough and cheaper this could mean the next evolution of storing data and
-abandoning classical hard and solid state drives in data warehouses.
-As we currently stand this is still not viable but it is quite an amazing and
-cool technology.
-My interests in this field are purely in encoding processes and experimental
-testing mainly because I don't have the access to this expensive machines. My
-initial goal was to create a toolkit that can be used by everybody to encode
-their data into a proper DNA sequence.
-## Glossary
-**deoxyribose** A five-carbon sugar molecule with a hydrogen atom rather than a
-hydroxyl group in the 2′ position; the sugar component of DNA nucleotides.
-**double helix** The molecular shape of DNA in which two strands of nucleotides
-wind around each other in a spiral shape.
-**nitrogenous base** A nitrogen-containing molecule that acts as a base; often
-referring to one of the purine or pyrimidine components of nucleic acids.
-**phosphate group** A molecular group consisting of a central phosphorus atom
-bound to four oxygen atoms.
-**RGB** The RGB color model is an additive color model in which red, green and
-blue light are added together in various ways to reproduce a broad array of
-colors.
-**GCC** The GNU Compiler Collection is a compiler system produced by the GNU
-Project supporting various programming languages.
-## Data encoding
-**TL;DR:** Encoding involves the use of a code to change original data into a
-form that can be used by an external process.
-Encoding is the process of converting data into a format required for a number
-of information processing needs, including:
- Program compiling and execution
- Data transmission, storage and compression/decompression
- Application data processing, such as file conversion
-Encoding can have two meanings:
- In computer technology, encoding is the process of applying a specific code,
-  such as letters, symbols and numbers, to data for conversion into an
-  equivalent cipher.
- In electronics, encoding refers to analog to digital conversion.
-## Quick history of DNA
- **1869** - Friedrich Miescher identifies "nuclein".
- **1900s** - The Eugenics Movement.
- **1900** – Mendel's theories are rediscovered by researchers.
- **1944** - Oswald Avery identifies DNA as the 'transforming principle'.
- **1952** - Rosalind Franklin photographs crystallized DNA fibres.
- **1953** - James Watson and Francis Crick discover the double helix structure of DNA.
- **1965** - Marshall Nirenberg is the first person to sequence the bases in each codon.
- **1983** - Huntington's disease is the first mapped genetic disease.
- **1990** - The Human Genome Project begins.
- **1995** - Haemophilus Influenzae is the first bacterium genome sequenced.
- **1996** - Dolly the sheep is cloned.
- **1999** - First human chromosome is decoded.
- **2000** – Genetic code of the fruit fly is decoded.
- **2002** – Mouse is the first mammal to have its genome decoded.
- **2003** – The Human Genome Project is completed.
- **2013** – DNA Worldwide and Eurofins Forensic discover identical twins have differences in their genetic makeup.
-## What is DNA?
-Deoxyribonucleic acid, a self-replicating material which is **present in nearly
-all living organisms** as the main constituent of chromosomes. It is the
-**carrier of genetic information**.
-> The nitrogen in our DNA, the calcium in our teeth, the iron in our blood,
-> the carbon in our apple pies were made in the interiors of collapsing stars.
-> We are made of starstuff.
-> **-- Carl Sagan, Cosmos**
-The nucleotide in DNA consists of a sugar (deoxyribose), one of four bases
-(cytosine (C), thymine (T), adenine (A), guanine (G)), and a phosphate.
-Cytosine and thymine are pyrimidine bases, while adenine and guanine are purine
-bases. The sugar and the base together are called a nucleoside.
-![DNA](/assets/posts/dna-sequence/dna-basics.jpg){:loading="lazy"}
-*DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and
-cytosine pairs with guanine. (credit a: modification of work by Jerome Walker,
-Dennis Myts)*
-## Encode binary data into DNA sequence
-As an input file you can use any file you want:
- ASCII files,
- Compiled programs,
- Multimedia files (MP3, MP4, MVK, etc),
- Images,
- Database files,
- etc.
-Note: If you would copy all the bytes from RAM to file or pipe data to file you
-could encode also this data as long as you provide file pointer to the encoder.
-### Basic Encoding
-As already mentioned, the Basic Encoding is based on a simple mapping. Since DNA
-is composed of 4 nucleotides (Adenine, Cytosine, Guanine, Thymine; usually
-referred using the first letter). Using this technique we can encode
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-using a single nucleotide. In this way, we are able to use the 4 bases that
-compose the DNA strand to encode each byte of data.
-| Two bits | Nucleotides      |
-| -------- | ---------------- |
-| 00       | **A** (Adenine)  |
-| 10       | **G** (Guanine)  |
-| 01       | **C** (Cytosine) |
-| 11       | **T** (Thymine)  |
-With this in mind we can simply encode any data by using two-bit to Nucleotides
-conversion.
-```python
-{ Algorithm 1: Naive byte array to DNA encode }
-procedure EncodeToDNASequence(f) string
-begin
-  enc string
-  while not eof(f) do
-    c byte := buffer[0]                             { Read 1 byte from buffer }
-    bin integer := sprintf('08b', c)                { Convert to string binary }
-    for e in range[0, 2, 4, 6] do
-      if e[0] == 48 and e[1] == 48 then             { 0x00 - A (Adenine) }
-        enc += 'A'
-      else if e[0] == 48 and e[1] == 49 then        { 0x01 - G (Guanine) }
-        enc += 'G'
-      else if e[0] == 49 and e[1] == 48 then        { 0x10 - C (Cytosine) }
-        enc += 'C'
-      else if e[0] == 49 and e[1] == 49 then        { 0x11 - T (Thymine) }
-        enc += 'T'
-  return enc                                        { Return DNA sequence }
-end
-```
-Another encoding would be **Goldman encoding**. Using this encoding helps with
-Nonsense mutation (amino acids replaced by a stop codon) that occurs and is the
-most problematic during translation because it leads to truncated amino acid
-sequences, which in turn results in truncated proteins.
-[Where to store big data? In DNA: Nick Goldman at TEDxPrague](https://www.youtube.com/watch?v=a4PiGWNsIEU)
-### FASTA file format
-In bioinformatics, FASTA format is a text-based format for representing either
-nucleotide sequences or peptide sequences, in which nucleotides or amino acids
-are represented using single-letter codes. The format also allows for sequence
-names and comments to precede the sequences. The format originates from the
-FASTA software package, but has now become a standard in the field of
-bioinformatics.
-The first line in a FASTA file started either with a ">" (greater-than) symbol
-or, less frequently, a ";" (semicolon) was taken as a comment. Subsequent lines
-starting with a semicolon would be ignored by software. Since the only comment
-used was the first, it quickly became used to hold a summary description of the
-sequence, often starting with a unique library accession number, and with time
-it has become commonplace to always use ">" for the first line and to not use
-";" comments (which would otherwise be ignored).
-```txt
-;LCBO - Prolactin precursor - Bovine
-; a sample sequence in FASTA format
-MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS
-EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL
-VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED
-ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*
->MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
-ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
-FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
-DIDGDGQVNYEEFVQMMTAK*
->gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
-LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
-EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
-LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
-GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
-IENY
-```
-FASTA format was extended by [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format)
-format from the [Sanger Centre](https://www.sanger.ac.uk/) in Cambridge.
-### PNG encoded DNA sequence
-| Nucleotides  | RGB         | Color name |
-| ------------ | ----------- | ---------- |
-| A ➞ Adenine  | (0,0,255)   | Blue       |
-| G ➞ Guanine  | (0,100,0)   | Green      |
-| C ➞ Cytosine | (255,0,0)   | Red        |
-| T ➞ Thymine  | (255,255,0) | Yellow     |
-With this in mind we can create a simple algorithm to create PNG representation
-of a DNA sequence.
-```python
-{ Algorithm 2: Naive DNA to PNG encode from FASTA file }
-procedure EncodeDNASequenceToPNG(f)
-begin
-  i image
-  while not eof(f) do
-    c char := buffer[0]                             { Read 1 char from buffer }
-    case c of
-      'A': color := RGB(0, 0, 255)                  { Blue }
-      'G': color := RGB(0, 100, 0)                  { Green }
-      'C': color := RGB(255, 0, 0)                  { Red }
-      'T': color := RGB(255, 255, 0)                { Yellow }
-    drawRect(i, [x, y], color)
-  save(i)                                           { Save PNG image }
-end
-```
-## Encoding text file in practice
-In this example we will take a simple text file as our input stream for
-encoding. This file will have a quote from Niels Bohr and saved as txt file.
-> How wonderful that we have met with a paradox. Now we have some hope of
-> making progress.
-> ― Niels Bohr
-First we encode text file into FASTA file.
-```bash
-./dnae-encode -i quote.txt -o quote.fa
-2019/01/10 00:38:29 Gathering input file stats
-2019/01/10 00:38:29 Starting encoding ...
- 106 B / 106 B [==================================] 100.00% 0s
-2019/01/10 00:38:29 Saving to FASTA file ...
-2019/01/10 00:38:29 Output FASTA file length is 438 B
-2019/01/10 00:38:29 Process took 987.263µs
-2019/01/10 00:38:29 Done ...
-```
-Output of `quote.fa` file contains the encoded DNA sequence in ASCII format.
-```txt
->SEQ1
-GACAGCTTGTGTACAAGTGTGCTTGCTCGCGAGCGGGTACGCGCGTGGGCTAACAAGTGA
-GCCAGCAGGTGAACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGCTGGCGGGTGA
-ACAAGTGTGCCGGTGAGCCAACAAGCAGACAAGTAAGCAGGTACGCAGGCGAGCTTGTCA
-ACTCACAAGATCGCTTGTGTACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGTAT
-GCTTGCTGGCGGACAAGCCAGCTTGTAAGCGGACAAGCTTGCGCACAAGCTGGCAGGCCT
-GCCGGCTCGCGTACAAATTCACAAGTAAGTACGCTTGCGTGTACGCGGGTATGTATACTC
-AACCTCACCAAACGGGACAAGATCGCCGGCGGGCTAGTATACAAGAACGCTTGCCAGTAC
-AACC
-```
-Then we encode FASTA file from previous operation to encode this data into PNG.
-```bash
-./dnae-png -i quote.fa -o quote.png
-2019/01/10 00:40:09 Gathering input file stats ...
-2019/01/10 00:40:09 Deconstructing FASTA file ...
-2019/01/10 00:40:09 Compositing image file ...
- 424 / 424 [==================================] 100.00% 0s
-2019/01/10 00:40:09 Saving output file ...
-2019/01/10 00:40:09 Output image file length is 1.1 kB
-2019/01/10 00:40:09 Process took 19.036117ms
-2019/01/10 00:40:09 Done ...
-```
-After encoding into PNG format this file looks like this.
-![Encoded Quote in PNG format](/assets/posts/dna-sequence/quote.png){:loading="lazy"}
-The larger the input stream is the larger the PNG file would be.
-Compiled basic Hello World C program with
-[GCC](https://www.gnu.org/software/gcc/) would [look
-like](/assets/posts/dna-sequence/sample.png).
-```c
-// gcc -O3 -o sample sample.c
-#include <stdio.h>
-main() {
-  printf("Hello, world!\n");
-  return 0;
-}
-```
-## Toolkit for encoding data
-I have created a toolkit with two main programs:
- dnae-encode (encodes file into FASTA file)
- dnae-png (encodes FASTA file into PNG)
-Toolkit with full source code is available on
-[github.com/mitjafelicijan/dna-encoding](https://github.com/mitjafelicijan/dna-encoding).
-### dnae-encode
-```bash
-> ./dnae-encode --help
-usage: dnae-encode --input=INPUT [<flags>]
-A command-line application that encodes file into DNA sequence.
-Flags:
-      --help             Show context-sensitive help (also try --help-long and --help-man).
-  -i, --input=INPUT      Input file (ASCII or binary) which will be encoded into DNA sequence.
-  -o, --output="out.fa"  Output file which stores DNA sequence in FASTA format.
-  -s, --sequence=SEQ1    The description line (defline) or header/identifier line, gives a name and/or a unique identifier for the sequence.
-  -c, --columns=60       Row characters length (no more than 120 characters). Devices preallocate fixed line sizes in software.
-      --version          Show application version.
-```
-### dnae-png
-```bash
-> ./dnae-png --help
-usage: dnae-png --input=INPUT [<flags>]
-A command-line application that encodes FASTA file into PNG image.
-Flags:
-      --help              Show context-sensitive help (also try --help-long and --help-man).
-  -i, --input=INPUT       Input FASTA file which will be encoded into PNG image.
-  -o, --output="out.png"  Output file in PNG format that represents DNA sequence in graphical way.
-  -s, --size=10           Size of pairings of DNA bases on image in pixels (lower resolution lower file size).
-      --version           Show application version.
-```
-## Benchmarks
-First we generate some binary sample data with dd.
-```bash
-dd if=<(openssl enc -aes-256-ctr  -pass pass:"$(dd if=/dev/urandom bs=128 count=1 2>/dev/null | base64)" -nosalt < /dev/zero) of=1KB.bin bs=1KB count=1 iflag=fullblock
-```
-![Sample binary file 1KB](/assets/posts/dna-sequence/sample-binary-file.png){:loading="lazy"}
-Our freshly generated 1KB file looks something like this (its full of
-garbage data as intended).
-We create following binary files:
- 1KB.bin
- 10KB.bin
- 100KB.bin
- 1MB.bin
- 10MB.bin
- 100MB.bin
-After this we create FASTA files for all the binary files by encoding them
-into DNA sequence.
-```bash
-./dnae-encode -i 100MB.bin -o 100MB.fa
-```
-Then we GZIP all the FASTA files to see how much the can be compressed.
-```bash
-gzip -9 < 10MB.fa > 10MB.fa.gz
-```
-![Encode to FASTA](/assets/posts/dna-sequence/chart-speed.svg){:loading="lazy"}
-The speed increase that occurs when encoding to FASTA format.
-![File sizes](/assets/posts/dna-sequence/chart-size.svg){:loading="lazy"}
-Size of the out file after encoding.
-[Download CSV file with benchmarks](/assets/posts/dna-sequence/benchmarks.csv).
-## References
- https://www.techopedia.com/definition/948/encoding
- https://www.dna-worldwide.com/resource/160/history-dna-timeline
- https://opentextbc.ca/biology/chapter/9-1-the-structure-of-dna/
- https://arxiv.org/abs/1801.04774
- https://en.wikipedia.org/wiki/FASTA_format