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authorMitja Felicijan <mitja.felicijan@gmail.com>2023-10-29 14:41:39 +0100
committerMitja Felicijan <mitja.felicijan@gmail.com>2023-10-29 14:41:39 +0100
commit2836163e54e3b94342113314e70ee564c456c43e (patch)
tree59b82fc69e83cc6d92846a8e9f510b0bb865cf3b /public/encoding-binary-data-into-dna-sequence.html
parentd50ea4053ea04abb3a455606d4591a8283af0677 (diff)
downloadmitjafelicijan.com-2836163e54e3b94342113314e70ee564c456c43e.tar.gz
Added public folder to git so it get get deployed on vercel
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1<!doctype html><html lang=en-us><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1"><link href="data:image/x-icon;base64,AAABAAEAEBAAAAEAIABoBAAAFgAAACgAAAAQAAAAIAAAAAEAIAAAAAAAAAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAL69vf8AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAv76+/8LBwQkAAAAAAAAAAAAAAAC+vb3/AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAL+9vf/Bv78JAAAAAAAAAAAAAAAAu7q6/wAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC7ubr/vr29CAAAAAAAAAAAy8nJAZ6foP8AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAnqGj/6GipAoAAAAAHLjU/xcXHf/BwsL/I8XY/yPK3v8XGiD/IbjL/yPF2f8XGiD/Fxkf/yLF2f8gnK3/Fxog/62ztv8fwNf/FRcd/x271v8mz93/GRsi/xkXHf8p097/GiIp/xobIv8p0t3/KdPe/xocIv8fYmr/KNPe/xoZH/8aHCL/J87c/xy81/8VFxz/IsPZ/8zS0/8XGiD/Ir/R/yPH2/8XGiD/Fxkf/yPH2/8dd4T/GBog/yPJ3f8jyNr/uru9/xcUGv8cudb/EhITDKi5vRKlvMP/RUpOERwcHRAdOj4QHTk8EBwdHRAdNTgQHTo/EBwcHRAcHB0QSGduEKW4vf+koqQfHzg+EBqz0ewSFRv7EyMr/xq51vsTERb7ExUb+xq41fsau9j7ExUb+xiPp/sZudb7ExUb+xMVG/sZuNX/GKvI/BIUGfMdvdn/IrfL/xcaIP8n1eb/J9Dh/xkcIf8ZGR7/J8/f/xxCSv8ZGyH/J9Dg/ybQ4P8ZHCL/FSQs/yPK3/8UExj/GE1b/ybS5P8ZGB7/Ghwj/ynW5P8p2Ob/Ghwi/yWrtv8p1eH/Ghwi/xocIv8p1uT/J8XT/xkcIv8m1un/Hb7d/xUYH/8hzOr/HtHu/xcaIf8XGB//I8vi/xgxOv8XGSD/I8rg/yPK4P8XGiD/GUFL/yPP6f8SERj/Fhkh/x3A4f8AAAAAJ2f9/ydr//8mZPH/AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAlYu38J2v//ydo/f8AAAAAAAAAAAd8/fkFqf//Iob8sAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAMY39awWr//8FfP3/AAAAAAAAAAAFm/7/SfD//wR+/f8AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAOB/f9B7v//BaX+/wAAAAAAAAAAQ878SAyZ/v9n1v4KAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADu9v8DDJb+/z3N/XgAAAAA3/sAAN/7AADf+wAA3/sAAAAAAAAAAAAAAAAAAN/7AAAAAAAAAAAAAAAAAAAAAAAAj/EAAI/5AACP8QAA3/sAAA==" rel=icon type=image/x-icon><title>Encoding binary data into DNA sequence</title><meta name=description content="Initial thoughtsImagine a world where you could go outside and take a leaf from a tree and putit through your personal DNA sequencer and get data like music, videos orcomputer programs from it."><link rel=alternate type=application/rss+xml title="Mitja Felicijan's posts" href=https://mitjafelicijan.com/index.xml><link rel=alternate type=application/rss+xml title="Mitja Felicijan's notes" href=https://mitjafelicijan.com/notes.xml><style>body{padding:1rem;max-width:760px;background:#fff;font-family:sans-serif;line-height:1.35rem;font-size:16px;margin:0 auto}hr{margin-block-start:1.5rem}h1,h2,h3{line-height:initial}h1{font-size:xx-large}footer{margin-block-start:2rem}cap{text-transform:capitalize}table{max-width:100%;width:100%;border-collapse:separate;border-spacing:2px;border:1px solid #000;border-left:1px solid #999;border-top:1px solid #999}blockquote{font-style:italic}table thead{background:#eee}ul.list li{padding:.2em 0}ul{line-height:1.4em}td,th{border:1px solid #000;padding:4px;border-right:1px solid #999;border-bottom:1px solid #999;text-align:left}pre{text-wrap:nowrap;overflow-x:auto;padding:0 1em;border:1px solid #dcdcdc}code{padding:0 3px;font-size:14px;border:0}pre code{line-height:1.3em}pre,code,pre *,code *{font-family:monospace}figure{margin-inline-start:0;margin-inline-end:0}figcaption{text-align:center}figcaption p{margin:.3em 0 0}img,video,audio{max-width:100%}header{display:flex;flex-direction:row;gap:3rem}nav{display:flex;gap:.75rem}nav.main{flex-grow:1}.pstatus-orange{background:gold}.pstatus-green{background:#9acd32}.pstatus-red{background:#cd5c5c}@media only screen and (max-width:600px){body{padding:15px}header{flex-direction:column;gap:1rem}a{word-wrap:break-word}}</style><header><nav class=main itemscope itemtype=http://schema.org/SiteNavigationElement role=toolbar><a href=/>Home</a>
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7<a href=/index.xml target=_blank>RSS</a></nav></header><main role=main><article itemtype=http://schema.org/Article><h1 itemtype=headline>Encoding binary data into DNA sequence</h1><p><cap>post</cap>, Jan 3, 2019 on <a href=https://mitjafelicijan.com>Mitja Felicijan's blog</a><div><h2 id=initial-thoughts>Initial thoughts</h2><p>Imagine a world where you could go outside and take a leaf from a tree and put
8it through your personal DNA sequencer and get data like music, videos or
9computer programs from it. Well, this is all possible now. It was not done on a
10large scale because it is quite expensive to create DNA strands but it's
11possible.<p>Encoding data into DNA sequence is relatively simple process once you understand
12the relationship between binary data and nucleotides and scientists have been
13making large leaps in this field in order to provide viable long-term storage
14solution for our data that would potentially survive our specie if case of
15global disaster. We could imprint all the world's knowledge into plants and
16ensure the survival of our knowledge.<p>More optimistic usage for this technology would be easier storage of ever
17growing data we produce every day. Once machines for sequencing DNA become fast
18enough and cheaper this could mean the next evolution of storing data and
19abandoning classical hard and solid state drives in data warehouses.<p>As we currently stand this is still not viable but it is quite an amazing and
20cool technology.<p>My interests in this field are purely in encoding processes and experimental
21testing mainly because I don't have the access to this expensive machines. My
22initial goal was to create a toolkit that can be used by everybody to encode
23their data into a proper DNA sequence.<h2 id=glossary>Glossary</h2><p><strong>deoxyribose</strong> A five-carbon sugar molecule with a hydrogen atom rather than a
24hydroxyl group in the 2′ position; the sugar component of DNA nucleotides.<p><strong>double helix</strong> The molecular shape of DNA in which two strands of nucleotides
25wind around each other in a spiral shape.<p><strong>nitrogenous base</strong> A nitrogen-containing molecule that acts as a base; often
26referring to one of the purine or pyrimidine components of nucleic acids.<p><strong>phosphate group</strong> A molecular group consisting of a central phosphorus atom
27bound to four oxygen atoms.<p><strong>RGB</strong> The RGB color model is an additive color model in which red, green and
28blue light are added together in various ways to reproduce a broad array of
29colors.<p><strong>GCC</strong> The GNU Compiler Collection is a compiler system produced by the GNU
30Project supporting various programming languages.<h2 id=data-encoding>Data encoding</h2><p><strong>TL;DR:</strong> Encoding involves the use of a code to change original data into a
31form that can be used by an external process.<p>Encoding is the process of converting data into a format required for a number
32of information processing needs, including:<ul><li>Program compiling and execution<li>Data transmission, storage and compression/decompression<li>Application data processing, such as file conversion</ul><p>Encoding can have two meanings:<ul><li>In computer technology, encoding is the process of applying a specific code,
33such as letters, symbols and numbers, to data for conversion into an
34equivalent cipher.<li>In electronics, encoding refers to analog to digital conversion.</ul><h2 id=quick-history-of-dna>Quick history of DNA</h2><ul><li><strong>1869</strong> - Friedrich Miescher identifies "nuclein".<li><strong>1900s</strong> - The Eugenics Movement.<li><strong>1900</strong> – Mendel's theories are rediscovered by researchers.<li><strong>1944</strong> - Oswald Avery identifies DNA as the 'transforming principle'.<li><strong>1952</strong> - Rosalind Franklin photographs crystallized DNA fibres.<li><strong>1953</strong> - James Watson and Francis Crick discover the double helix structure of DNA.<li><strong>1965</strong> - Marshall Nirenberg is the first person to sequence the bases in each codon.<li><strong>1983</strong> - Huntington's disease is the first mapped genetic disease.<li><strong>1990</strong> - The Human Genome Project begins.<li><strong>1995</strong> - Haemophilus Influenzae is the first bacterium genome sequenced.<li><strong>1996</strong> - Dolly the sheep is cloned.<li><strong>1999</strong> - First human chromosome is decoded.<li><strong>2000</strong> – Genetic code of the fruit fly is decoded.<li><strong>2002</strong> – Mouse is the first mammal to have its genome decoded.<li><strong>2003</strong> – The Human Genome Project is completed.<li><strong>2013</strong> – DNA Worldwide and Eurofins Forensic discover identical twins have differences in their genetic makeup.</ul><h2 id=what-is-dna>What is DNA?</h2><p>Deoxyribonucleic acid, a self-replicating material which is <strong>present in nearly
35all living organisms</strong> as the main constituent of chromosomes. It is the
36<strong>carrier of genetic information</strong>.<blockquote><p>The nitrogen in our DNA, the calcium in our teeth, the iron in our blood,
37the carbon in our apple pies were made in the interiors of collapsing stars.
38We are made of starstuff.
39<strong>-- Carl Sagan, Cosmos</strong></blockquote><p>The nucleotide in DNA consists of a sugar (deoxyribose), one of four bases
40(cytosine (C), thymine (T), adenine (A), guanine (G)), and a phosphate.
41Cytosine and thymine are pyrimidine bases, while adenine and guanine are purine
42bases. The sugar and the base together are called a nucleoside.<figure><img src=/posts/dna-sequence/dna-basics.jpg alt=DNA><figcaption><p><em>DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and
43cytosine pairs with guanine. (credit a: modification of work by Jerome Walker,
44Dennis Myts)</em></figcaption></figure><h2 id=encode-binary-data-into-dna-sequence>Encode binary data into DNA sequence</h2><p>As an input file you can use any file you want:<ul><li>ASCII files,<li>Compiled programs,<li>Multimedia files (MP3, MP4, MVK, etc),<li>Images,<li>Database files,<li>etc.</ul><p>Note: If you would copy all the bytes from RAM to file or pipe data to file you
45could encode also this data as long as you provide file pointer to the encoder.<h3 id=basic-encoding>Basic Encoding</h3><p>As already mentioned, the Basic Encoding is based on a simple mapping. Since DNA
46is composed of 4 nucleotides (Adenine, Cytosine, Guanine, Thymine; usually
47referred using the first letter). Using this technique we can encode</p><center><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 -907.9672135000189 11313.37788460873 1185.0382429179317" style="width: 26.259ex; height: 2.721ex; vertical-align: -0.68ex; margin: 1px 0px;"><g stroke="black" fill="black" stroke-width="0" transform="matrix(1 0 0 -1 0 0)"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMATHI-6C"/><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMATHI-6F" x="303" y="0"/><g transform="translate(793,0)"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMATHI-67"/><use transform="scale(0.7071067811865476)" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMAIN-32" x="681" y="-213"/></g><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMAIN-28" x="1732" y="0"/><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMAIN-34" x="2126" y="0"/><use xmlns:xlink="http://www.w3.org/1999/xlink" 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431H323Q330 424 330 420Q330 398 317 385H210L174 240Q135 80 135 68Q135 26 162 26Q197 26 230 60T283 144Q285 150 288 151T303 153H307Q322 153 322 145Q322 142 319 133Q314 117 301 95T267 48T216 6T155 -11Q125 -11 98 4T59 56Q57 64 57 83V101L92 241Q127 382 128 383Q128 385 77 385H26Z"/><path id="MJMATHI-73" stroke-width="10" d="M131 289Q131 321 147 354T203 415T300 442Q362 442 390 415T419 355Q419 323 402 308T364 292Q351 292 340 300T328 326Q328 342 337 354T354 372T367 378Q368 378 368 379Q368 382 361 388T336 399T297 405Q249 405 227 379T204 326Q204 301 223 291T278 274T330 259Q396 230 396 163Q396 135 385 107T352 51T289 7T195 -10Q118 -10 86 19T53 87Q53 126 74 143T118 160Q133 160 146 151T160 120Q160 94 142 76T111 58Q109 57 108 57T107 55Q108 52 115 47T146 34T201 27Q237 27 263 38T301 66T318 97T323 122Q323 150 302 164T254 181T195 196T148 231Q131 256 131 289Z"/></defs></svg></center><p>using a single nucleotide. In this way, we are able to use the 4 bases that
48compose the DNA strand to encode each byte of data.<table><thead><tr><th>Two bits<th>Nucleotides<tbody><tr><td>00<td><strong>A</strong> (Adenine)<tr><td>10<td><strong>G</strong> (Guanine)<tr><td>01<td><strong>C</strong> (Cytosine)<tr><td>11<td><strong>T</strong> (Thymine)</table><p>With this in mind we can simply encode any data by using two-bit to Nucleotides
49conversion.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>{ Algorithm 1: Naive byte array to DNA encode }
50</span></span><span style=display:flex><span>procedure EncodeToDNASequence(f) string
51</span></span><span style=display:flex><span>begin
52</span></span><span style=display:flex><span> enc string
53</span></span><span style=display:flex><span> <span style=color:#00f>while</span> <span style=color:#00f>not</span> eof(f) do
54</span></span><span style=display:flex><span> c byte := buffer[0] { Read 1 byte <span style=color:#00f>from</span> buffer }
55</span></span><span style=display:flex><span> bin integer := sprintf(<span style=color:#a31515>&#39;08b&#39;</span>, c) { Convert to string binary }
56</span></span><span style=display:flex><span> <span style=color:#00f>for</span> e <span style=color:#00f>in</span> range[0, 2, 4, 6] do
57</span></span><span style=display:flex><span> <span style=color:#00f>if</span> e[0] == 48 <span style=color:#00f>and</span> e[1] == 48 then { 0x00 - A (Adenine) }
58</span></span><span style=display:flex><span> enc += <span style=color:#a31515>&#39;A&#39;</span>
59</span></span><span style=display:flex><span> <span style=color:#00f>else</span> <span style=color:#00f>if</span> e[0] == 48 <span style=color:#00f>and</span> e[1] == 49 then { 0x01 - G (Guanine) }
60</span></span><span style=display:flex><span> enc += <span style=color:#a31515>&#39;G&#39;</span>
61</span></span><span style=display:flex><span> <span style=color:#00f>else</span> <span style=color:#00f>if</span> e[0] == 49 <span style=color:#00f>and</span> e[1] == 48 then { 0x10 - C (Cytosine) }
62</span></span><span style=display:flex><span> enc += <span style=color:#a31515>&#39;C&#39;</span>
63</span></span><span style=display:flex><span> <span style=color:#00f>else</span> <span style=color:#00f>if</span> e[0] == 49 <span style=color:#00f>and</span> e[1] == 49 then { 0x11 - T (Thymine) }
64</span></span><span style=display:flex><span> enc += <span style=color:#a31515>&#39;T&#39;</span>
65</span></span><span style=display:flex><span> <span style=color:#00f>return</span> enc { Return DNA sequence }
66</span></span><span style=display:flex><span>end
67</span></span></code></pre><p>Another encoding would be <strong>Goldman encoding</strong>. Using this encoding helps with
68Nonsense mutation (amino acids replaced by a stop codon) that occurs and is the
69most problematic during translation because it leads to truncated amino acid
70sequences, which in turn results in truncated proteins.<p><a href="https://www.youtube.com/watch?v=a4PiGWNsIEU">Where to store big data? In DNA: Nick Goldman at TEDxPrague</a><h3 id=fasta-file-format>FASTA file format</h3><p>In bioinformatics, FASTA format is a text-based format for representing either
71nucleotide sequences or peptide sequences, in which nucleotides or amino acids
72are represented using single-letter codes. The format also allows for sequence
73names and comments to precede the sequences. The format originates from the
74FASTA software package, but has now become a standard in the field of
75bioinformatics.<p>The first line in a FASTA file started either with a ">" (greater-than) symbol
76or, less frequently, a ";" (semicolon) was taken as a comment. Subsequent lines
77starting with a semicolon would be ignored by software. Since the only comment
78used was the first, it quickly became used to hold a summary description of the
79sequence, often starting with a unique library accession number, and with time
80it has become commonplace to always use ">" for the first line and to not use
81";" comments (which would otherwise be ignored).<pre><code>;LCBO - Prolactin precursor - Bovine
82; a sample sequence in FASTA format
83MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS
84EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL
85VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED
86ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*
87
88&gt;MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
89ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
90FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
91DIDGDGQVNYEEFVQMMTAK*
92
93&gt;gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
94LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
95EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
96LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
97GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
98IENY
99</code></pre><p>FASTA format was extended by <a href=https://en.wikipedia.org/wiki/FASTQ_format>FASTQ</a>
100format from the <a href=https://www.sanger.ac.uk/>Sanger Centre</a> in Cambridge.<h3 id=png-encoded-dna-sequence>PNG encoded DNA sequence</h3><table><thead><tr><th>Nucleotides<th>RGB<th>Color name<tbody><tr><td>A ➞ Adenine<td>(0,0,255)<td>Blue<tr><td>G ➞ Guanine<td>(0,100,0)<td>Green<tr><td>C ➞ Cytosine<td>(255,0,0)<td>Red<tr><td>T ➞ Thymine<td>(255,255,0)<td>Yellow</table><p>With this in mind we can create a simple algorithm to create PNG representation
101of a DNA sequence.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>{ Algorithm 2: Naive DNA to PNG encode <span style=color:#00f>from</span> FASTA file }
102</span></span><span style=display:flex><span>procedure EncodeDNASequenceToPNG(f)
103</span></span><span style=display:flex><span>begin
104</span></span><span style=display:flex><span> i image
105</span></span><span style=display:flex><span> <span style=color:#00f>while</span> <span style=color:#00f>not</span> eof(f) do
106</span></span><span style=display:flex><span> c char := buffer[0] { Read 1 char <span style=color:#00f>from</span> buffer }
107</span></span><span style=display:flex><span> case c of
108</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;A&#39;</span>: color := RGB(0, 0, 255) { Blue }
109</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;G&#39;</span>: color := RGB(0, 100, 0) { Green }
110</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;C&#39;</span>: color := RGB(255, 0, 0) { Red }
111</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;T&#39;</span>: color := RGB(255, 255, 0) { Yellow }
112</span></span><span style=display:flex><span> drawRect(i, [x, y], color)
113</span></span><span style=display:flex><span> save(i) { Save PNG image }
114</span></span><span style=display:flex><span>end
115</span></span></code></pre><h2 id=encoding-text-file-in-practice>Encoding text file in practice</h2><p>In this example we will take a simple text file as our input stream for
116encoding. This file will have a quote from Niels Bohr and saved as txt file.<blockquote><p>How wonderful that we have met with a paradox. Now we have some hope of
117making progress.
118― Niels Bohr</blockquote><p>First we encode text file into FASTA file.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-encode -i quote.txt -o quote.fa
119</span></span><span style=display:flex><span>2019/01/10 00:38:29 Gathering input file stats
120</span></span><span style=display:flex><span>2019/01/10 00:38:29 Starting encoding ...
121</span></span><span style=display:flex><span> 106 B / 106 B [==================================] 100.00% 0s
122</span></span><span style=display:flex><span>2019/01/10 00:38:29 Saving to FASTA file ...
123</span></span><span style=display:flex><span>2019/01/10 00:38:29 Output FASTA file length is 438 B
124</span></span><span style=display:flex><span>2019/01/10 00:38:29 Process took 987.263µs
125</span></span><span style=display:flex><span>2019/01/10 00:38:29 Done ...
126</span></span></code></pre><p>Output of <code>quote.fa</code> file contains the encoded DNA sequence in ASCII format.<pre><code>&gt;SEQ1
127GACAGCTTGTGTACAAGTGTGCTTGCTCGCGAGCGGGTACGCGCGTGGGCTAACAAGTGA
128GCCAGCAGGTGAACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGCTGGCGGGTGA
129ACAAGTGTGCCGGTGAGCCAACAAGCAGACAAGTAAGCAGGTACGCAGGCGAGCTTGTCA
130ACTCACAAGATCGCTTGTGTACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGTAT
131GCTTGCTGGCGGACAAGCCAGCTTGTAAGCGGACAAGCTTGCGCACAAGCTGGCAGGCCT
132GCCGGCTCGCGTACAAATTCACAAGTAAGTACGCTTGCGTGTACGCGGGTATGTATACTC
133AACCTCACCAAACGGGACAAGATCGCCGGCGGGCTAGTATACAAGAACGCTTGCCAGTAC
134AACC
135</code></pre><p>Then we encode FASTA file from previous operation to encode this data into PNG.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-png -i quote.fa -o quote.png
136</span></span><span style=display:flex><span>2019/01/10 00:40:09 Gathering input file stats ...
137</span></span><span style=display:flex><span>2019/01/10 00:40:09 Deconstructing FASTA file ...
138</span></span><span style=display:flex><span>2019/01/10 00:40:09 Compositing image file ...
139</span></span><span style=display:flex><span> 424 / 424 [==================================] 100.00% 0s
140</span></span><span style=display:flex><span>2019/01/10 00:40:09 Saving output file ...
141</span></span><span style=display:flex><span>2019/01/10 00:40:09 Output image file length is 1.1 kB
142</span></span><span style=display:flex><span>2019/01/10 00:40:09 Process took 19.036117ms
143</span></span><span style=display:flex><span>2019/01/10 00:40:09 Done ...
144</span></span></code></pre><p>After encoding into PNG format this file looks like this.<figure><img src=/posts/dna-sequence/quote.png alt="Encoded Quote in PNG format"><figcaption><p>The larger the input stream is the larger the PNG file would be.</figcaption></figure><p>Compiled basic Hello World C program with
145<a href=https://www.gnu.org/software/gcc/>GCC</a> would <a href=/posts/dna-sequence/sample.png>look
146like</a>.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span><span style=color:green>// gcc -O3 -o sample sample.c
147</span></span></span><span style=display:flex><span><span style=color:green></span><span style=color:#00f>#include</span> <span style=color:#00f>&lt;stdio.h&gt;</span><span style=color:#00f>
148</span></span></span><span style=display:flex><span><span style=color:#00f></span>
149</span></span><span style=display:flex><span>main() {
150</span></span><span style=display:flex><span> printf(<span style=color:#a31515>&#34;Hello, world!</span><span style=color:#a31515>\n</span><span style=color:#a31515>&#34;</span>);
151</span></span><span style=display:flex><span> <span style=color:#00f>return</span> 0;
152</span></span><span style=display:flex><span>}
153</span></span></code></pre><h2 id=toolkit-for-encoding-data>Toolkit for encoding data</h2><p>I have created a toolkit with two main programs:<ul><li>dnae-encode (encodes file into FASTA file)<li>dnae-png (encodes FASTA file into PNG)</ul><p>Toolkit with full source code is available on
154<a href=https://github.com/mitjafelicijan/dna-encoding>github.com/mitjafelicijan/dna-encoding</a>.<h3 id=dnae-encode>dnae-encode</h3><pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>&gt; ./dnae-encode --help
155</span></span><span style=display:flex><span>usage: dnae-encode --input=INPUT [&lt;flags&gt;]
156</span></span><span style=display:flex><span>
157</span></span><span style=display:flex><span>A command-line application that encodes file into DNA sequence.
158</span></span><span style=display:flex><span>
159</span></span><span style=display:flex><span>Flags:
160</span></span><span style=display:flex><span> --help Show context-sensitive help (also try --help-long and --help-man).
161</span></span><span style=display:flex><span> -i, --input=INPUT Input file (ASCII or binary) which will be encoded into DNA sequence.
162</span></span><span style=display:flex><span> -o, --output=<span style=color:#a31515>&#34;out.fa&#34;</span> Output file which stores DNA sequence in FASTA format.
163</span></span><span style=display:flex><span> -s, --sequence=SEQ1 The description line (defline) or header/identifier line, gives a name and/or a unique identifier <span style=color:#00f>for</span> the sequence.
164</span></span><span style=display:flex><span> -c, --columns=60 Row characters length (no more than 120 characters). Devices preallocate fixed line sizes in software.
165</span></span><span style=display:flex><span> --version Show application version.
166</span></span></code></pre><h3 id=dnae-png>dnae-png</h3><pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>&gt; ./dnae-png --help
167</span></span><span style=display:flex><span>usage: dnae-png --input=INPUT [&lt;flags&gt;]
168</span></span><span style=display:flex><span>
169</span></span><span style=display:flex><span>A command-line application that encodes FASTA file into PNG image.
170</span></span><span style=display:flex><span>
171</span></span><span style=display:flex><span>Flags:
172</span></span><span style=display:flex><span> --help Show context-sensitive help (also try --help-long and --help-man).
173</span></span><span style=display:flex><span> -i, --input=INPUT Input FASTA file which will be encoded into PNG image.
174</span></span><span style=display:flex><span> -o, --output=<span style=color:#a31515>&#34;out.png&#34;</span> Output file in PNG format that represents DNA sequence in graphical way.
175</span></span><span style=display:flex><span> -s, --size=10 Size of pairings of DNA bases on image in pixels (lower resolution lower file size).
176</span></span><span style=display:flex><span> --version Show application version.
177</span></span></code></pre><h2 id=benchmarks>Benchmarks</h2><p>First we generate some binary sample data with dd.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>dd <span style=color:#00f>if</span>=&lt;(openssl enc -aes-256-ctr -pass pass:<span style=color:#a31515>&#34;</span><span style=color:#00f>$(</span>dd <span style=color:#00f>if</span>=/dev/urandom bs=128 count=1 2&gt;/dev/null | base64<span style=color:#00f>)</span><span style=color:#a31515>&#34;</span> -nosalt &lt; /dev/zero) of=1KB.bin bs=1KB count=1 iflag=fullblock
178</span></span></code></pre><p>Our freshly generated 1KB file looks something like this (its full of garbage
179data as intended).<figure><img src=/posts/dna-sequence/sample-binary-file.png alt="Sample binary file 1KB"></figure><p>We create following binary files:<ul><li>1KB.bin<li>10KB.bin<li>100KB.bin<li>1MB.bin<li>10MB.bin<li>100MB.bin</ul><p>After this we create FASTA files for all the binary files by encoding them
180into DNA sequence.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-encode -i 100MB.bin -o 100MB.fa
181</span></span></code></pre><p>Then we GZIP all the FASTA files to see how much the can be compressed.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>gzip -9 &lt; 10MB.fa &gt; 10MB.fa.gz
182</span></span></code></pre><figure><img src=/posts/dna-sequence/chart-speed.svg alt="Encode to FASTA"><figcaption><p>The speed increase that occurs when encoding to FASTA format.</figcaption></figure><figure><img src=/posts/dna-sequence/chart-size.svg alt="File sizes"><figcaption><p>Size of the out file after encoding.</figcaption></figure><p><a href=/posts/dna-sequence/benchmarks.csv>Download CSV file with benchmarks</a>.<h2 id=references>References</h2><ul><li><a href=https://www.techopedia.com/definition/948/encoding>https://www.techopedia.com/definition/948/encoding</a><li><a href=https://www.dna-worldwide.com/resource/160/history-dna-timeline>https://www.dna-worldwide.com/resource/160/history-dna-timeline</a><li><a href=https://opentextbc.ca/biology/chapter/9-1-the-structure-of-dna/>https://opentextbc.ca/biology/chapter/9-1-the-structure-of-dna/</a><li><a href=https://arxiv.org/abs/1801.04774>https://arxiv.org/abs/1801.04774</a><li><a href=https://en.wikipedia.org/wiki/FASTA_format>https://en.wikipedia.org/wiki/FASTA_format</a></ul></div></article></main><section><hr><h2>Posts from blogs I follow around the net</h2><ul><li><a href=https://chotrin.org/writing/2023-10-20.html target=_blank rel=noopener>OpenBSD upgrade and fall things.</a><div>Been AFK for a bit. It's autumn and I upgraded this server to OpenBSD 7.4! — <a href=https://chotrin.org>chötrin's wiki.</a><li><a href=https://mirzapandzo.com/next-image-url-parameter-is-valid-but-upstream-response-is-invalid target=_blank rel=noopener>Next/Image "url" parameter is valid but upstream response is invalid</a><div>Getting "url" parameter is valid but upstream response is invalid error with Next/Image on WSL2 — <a href=https://mirzapandzo.com/>Mirza Pandzo's Blog</a><li><a href=https://drewdevault.com/2023/10/13/Going-off-script.html target=_blank rel=noopener>Going off-script</a><div>There is a phenomenon in society which I find quite bizarre. Upon our entry to
183this mortal coil, we are endowed with self-awareness, agency, and free will.
184Each of th… — <a href=https://drewdevault.com>Drew DeVault's blog</a><li><a href=https://solar.lowtechmagazine.com/2023/10/workshop-in-rotterdam-how-to-build-a-bike-generator/ target=_blank rel=noopener>Workshop in Rotterdam: How to Build a Bike Generator</a><div>Afbeelding: Low-tech Magazine workshop in Rotterdam, the Netherlands. Poster: Marie Verdeil. Image: Sara Vercauteren
185The workshop takes place on behalf of the “Hou… — <a href=https://solar.lowtechmagazine.com/posts/>LOW←TECH MAGAZINE English</a><li><a href="http://offbeatpursuit.com:80/blog/?id=24" target=_blank rel=noopener>Printf debugging</a><div>tags:
186plan9
187There’s no shame in that. Yes, there is documentation, code to be
188read, and debuggers to be used. But sometimes you just need to “see”
189what is happening.
190So… — <a href=http://offbeatpursuit.com:80/blog/>WLOG - blog</a><li><a href=https://neil.computer/notes/chart-of-accounts-for-startups-and-saas-companies/ target=_blank rel=noopener>Chart of Accounts for Startups and SaaS Companies</a><div>Accounting is fundamental to starting a business. You need to have a basic understanding of accounting principles and essential bookkeeping. I had to learn it. Ther… — <a href=https://neil.computer/>Neil Panchal</a><li><a href=https://journal.valeriansaliou.name/deploy-a-nomad-cluster-on-alpine-linux-with-vultr/ target=_blank rel=noopener>Deploy a Nomad Cluster on Alpine Linux with Vultr</a><div>After spending countless hours trying to understand how to deploy my apps on Kubernetes for the first time to host Mirage, an AI API service that I run, I ended up … — <a href=https://journal.valeriansaliou.name/>Valerian Saliou</a><li><a href=https://jcs.org/2023/10/17/wikipedia target=_blank rel=noopener>Wikipedia Reader 1.0 Released</a><div>Wikipedia Reader
1911.0 has been released:
192wikipedia-1.0.sit
193(StuffIt 3 archive, includes
194source code
195and THINK C 5 project file)
196SHA256: 360e12d064f6579695f1e627ce34cb2f0… — <a href=https://jcs.org/>joshua stein</a></ul><p><a href=https://git.sr.ht/~sircmpwn/openring>Generated with openring.</a></section><footer><hr><p><big><strong>Want to comment or have something to add?</strong></big><p>You can write me an email
197at <a href=mailto:m@mitjafelicijan.com>m@mitjafelicijan.com</a> or
198catch up with me <a href=https://telegram.me/mitjafelicijan target=_blank>on Telegram</a>.<hr><p>This website does not track you. Content is made available under
199the <a href=https://creativecommons.org/licenses/by/4.0/ target=_blank rel=noreferrer>CC BY 4.0 license</a> unless specified
200otherwise. Blog is also available as <a href=/index.xml target=_blank>RSS feed</a>.</footer> \ No newline at end of file
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