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+---
+title: Encoding binary data into DNA sequence
+url: /encoding-binary-data-into-dna-sequence.html
+date: 2019-01-03T12:00:00+02:00
+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)
+
+*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)
+
+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)
+
+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)
+
+The speed increase that occurs when encoding to FASTA format.
+
+![File sizes](/assets/posts/dna-sequence/chart-size.svg)
+
+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