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authorMitja Felicijan <mitja.felicijan@gmail.com>2023-10-31 13:48:54 +0100
committerMitja Felicijan <mitja.felicijan@gmail.com>2023-10-31 13:48:54 +0100
commitfd3a6a3730d4078f6be4239a9c24c9747ef9d555 (patch)
tree074768d86f2d00c4c84410c61e71f5c55e08dc4c /public/encoding-binary-data-into-dna-sequence.html
parent7155ee3591cf1e610ec5e0f3de1c75be86cf0993 (diff)
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2<a href=/#posts>Posts</a> 2<a href=/#posts>Posts</a>
3<a href=/#notes>Notes</a> 3<a href=/#notes>Notes</a>
4<a href=/#sideprojects class=hob>Side Projects</a> 4<a href=/#sideprojects class=hob>Side Projects</a>
@@ -177,8 +177,8 @@ like</a>.<pre tabindex=0 style=background-color:#fff><code><span style=display:f
177</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). 177</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).
178</span></span><span style=display:flex><span> --version Show application version. 178</span></span><span style=display:flex><span> --version Show application version.
179</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>$(</span>dd <span style=color:#00f>if</span>=/dev/urandom bs=128 count=1 2&gt;/dev/null | base64<span style=color:#00f>)</span><span style=color:#a31515>&#34;</span> -nosalt &lt; /dev/zero) of=1KB.bin bs=1KB count=1 iflag=fullblock 179</span></span></code></pre><h2 id=benchmarks>Benchmarks</h2><p>First we generate some binary sample data with dd.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>dd <span style=color:#00f>if</span>=&lt;(openssl enc -aes-256-ctr -pass pass:<span style=color:#a31515>&#34;</span><span style=color:#00f>$(</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
180</span></span></code></pre><p>Our freshly generated 1KB file looks something like this (its full of garbage 180</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
181data as intended).<figure><img loading="lazy" 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 181garbage 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
182into DNA sequence.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-encode -i 100MB.bin -o 100MB.fa 182into DNA sequence.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-encode -i 100MB.bin -o 100MB.fa
183</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 183</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
184</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 184</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
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