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-<!doctype html><html lang=en-us><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1"><meta name=generator content="JBMAFP - github.com/mitjafelicijan/jbmafp"><link href="data:image/x-icon;base64,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" 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."><meta name=author content="Mitja Felicijan"><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>:root{--border-color:gainsboro;--border-size:2px;--link-color:blue;--bg-color:#eee}*::selection{background:var(--link-color);color:#fff}*::-moz-selection{background:var(--link-color);color:#fff}*::-webkit-selection{background:var(--link-color);color:#fff}body{padding:2.5rem;max-width:1900px;background:#fff;font-family:sans-serif;line-height:1.35rem;font-size:16px}hr{border:0;border-bottom:var(--border-size)solid var(--border-color);margin-block-start:1.5rem}a{color:var(--link-color);text-decoration:none}h1,h2,h3{line-height:initial}h1{font-size:xx-large}footer{margin-block-start:2rem}cap{text-transform:capitalize}blockquote{font-style:italic}table{max-width:100%;border:var(--border-size)solid var(--border-color);border-collapse:separate;border-spacing:0}table thead tr th{border-bottom:var(--border-size)solid var(--border-color);text-align:left}table th,table td{padding:.5em .8em}ul.list li{padding:.2em 0}ul{line-height:1.35em}pre{text-wrap:nowrap;overflow-x:auto;padding:0 1em;border:var(--border-size)solid var(--border-color)}code{padding:0 3px;font-size:14px;border:0;background:var(--bg-color)}pre code{line-height:1.3em;background:#fff}pre,code,pre *,code *{font-family:monospace}figure{margin-inline-start:0;margin-inline-end:0}figcaption{width:800px;max-width:100%;text-align:center}figcaption p{margin:.3em 0 1.5em;font-style:italic}img,video,audio{width:800px;max-width:100%;border:var(--border-size)solid var(--border-color);padding:.5em}header nav{display:flex;gap:.9rem}article iframe{margin:0!important}audio::-webkit-media-controls-enclosure{border-radius:0}@media only screen and (max-width:600px){body{padding:.5em;word-wrap:break-word}header nav{gap:.7rem}header nav .hob{display:none}a{word-wrap:break-word}}</style><header><nav class=main itemscope itemtype=http://schema.org/SiteNavigationElement role=toolbar><a href=/>Home</a>
+<!doctype html><html lang=en-us><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1"><meta name=generator content="JBMAFP - github.com/mitjafelicijan/jbmafp"><link href="data:image/x-icon;base64,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" 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."><meta name=author content="Mitja Felicijan"><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>:root{--border-color:gainsboro;--border-size:2px;--link-color:blue;--bg-color:#eee}*::selection{background:var(--link-color);color:#fff}*::-moz-selection{background:var(--link-color);color:#fff}*::-webkit-selection{background:var(--link-color);color:#fff}body{padding:2.5rem;max-width:1900px;background:#fff;font-family:sans-serif;line-height:1.35rem;font-size:16px}hr{border:0;border-bottom:var(--border-size)solid var(--border-color);margin-block-start:1.5rem}a{color:var(--link-color);text-decoration:none}h1,h2,h3{line-height:initial}h1{font-size:xx-large}footer{margin-block-start:2rem}cap{text-transform:capitalize}blockquote{font-style:italic}table{max-width:100%;border:var(--border-size)solid var(--border-color);border-collapse:separate;border-spacing:0}table thead tr th{border-bottom:var(--border-size)solid var(--border-color);text-align:left}table th,table td{padding:.5em .8em}ul.list li{padding:.2em 0}ul{line-height:1.35em}pre{text-wrap:nowrap;overflow-x:auto;padding:0 1em;border:var(--border-size)solid var(--border-color)}code{padding:0 3px;font-size:14px;border:0;background:var(--bg-color)}pre code{line-height:1.3em;background:#fff}pre,code,pre *,code *{font-family:monospace}figure{margin-inline-start:0;margin-inline-end:0}figcaption{width:800px;max-width:100%;text-align:center}figcaption p{margin:.3em 0 1.5em;font-style:italic}img,video,audio{width:800px;max-width:100%;border:var(--border-size)solid var(--border-color);padding:.5em}header nav{display:flex;gap:.9rem}article iframe{margin:0!important}audio::-webkit-media-controls-enclosure{border-radius:0}@media only screen and (max-width:600px){body{padding:.5em;word-wrap:break-word}header nav{gap:.7rem}header nav .hob{display:none}a{word-wrap:break-word}}</style><header><nav class=main itemscope itemtype=http://schema.org/SiteNavigationElement role=navigation aria-label="Main navigation"><a href=/>Home</a>
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@@ -41,7 +41,7 @@ We are made of starstuff.
 <strong>-- Carl Sagan, Cosmos</strong></blockquote><p>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.<figure><img loading="lazy" 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
+bases. 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
 cytosine pairs with guanine. (credit a: modification of work by Jerome Walker,
 Dennis 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
 could 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
@@ -143,7 +143,7 @@ making progress.
 </span></span><span style=display:flex><span>2019/01/10 00:40:09 Output image file length is 1.1 kB
 </span></span><span style=display:flex><span>2019/01/10 00:40:09 Process took 19.036117ms
 </span></span><span style=display:flex><span>2019/01/10 00:40:09 Done ...
-</span></span></code></pre><p>After encoding into PNG format this file looks like this.<figure><img loading="lazy" 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
+</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
 <a href=https://www.gnu.org/software/gcc/>GCC</a> would <a href=/posts/dna-sequence/sample.png>look
 like</a>.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span><span style=color:green>// gcc -O3 -o sample sample.c
 </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>
@@ -177,11 +177,11 @@ like</a>.<pre tabindex=0 style=background-color:#fff><code><span style=display:f
 </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).
 </span></span><span style=display:flex><span>      --version           Show application version.
 </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
-</span></span></code></pre><figure><img loading="lazy" src=/posts/dna-sequence/sample-binary-file.png alt="Sample binary file 1KB"><figcaption><p>Our freshly generated 1KB file looks something like this (its full of
+</span></span></code></pre><figure><img src=/posts/dna-sequence/sample-binary-file.png alt="Sample binary file 1KB"><figcaption><p>Our freshly generated 1KB file looks something like this (its full of
 garbage data as intended).</figcaption></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
 into DNA sequence.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-encode -i 100MB.bin -o 100MB.fa
 </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
-</span></span></code></pre><figure><img loading="lazy" 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 loading="lazy" 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://utcc.utoronto.ca/~cks/space/blog/linux/NFSv4ServerLockClients target=_blank rel=noopener>Finding which NFSv4 client owns a lock on a Linux NFS(v4) server</a> — <a href=https://utcc.utoronto.ca/~cks/space/blog/>Chris's Wiki :: blog</a><div>A while back I wrote an entry about finding which NFS client owns
+</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://utcc.utoronto.ca/~cks/space/blog/linux/NFSv4ServerLockClients target=_blank rel=noopener>Finding which NFSv4 client owns a lock on a Linux NFS(v4) server</a> — <a href=https://utcc.utoronto.ca/~cks/space/blog/>Chris's Wiki :: blog</a><div>A while back I wrote an entry about finding which NFS client owns
 a lock on a Linux NFS server, which turned
 out to be specific to NFS v3 (which I really should have seen coming,
 since it involved NLM and lockd). Finding the NFS v4 client that