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fluentdna.html
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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="">
<title>Fluent DNA</title>
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content="https://getbootstrap.com/docs/4.4/assets/img/favicons/browserconfig.xml">
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font-size: 1.125rem;
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font-size: 3.5rem;
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<!-- Custom styles for this template -->
<link href="album.css" rel="stylesheet">
</head>
<body>
<header>
<div class="collapse bg-dark" id="navbarHeader">
<div class="container">
<div class="row">
<div class="col-sm-8 col-md-7 py-4">
<h4 class="text-white">About</h4>
<p class="text-muted">FluentDNA visualizes sequence data with nucleotides as colors in a 2D layout with a zoomable interface. The layout can scale to accommodate any number of chromosomes and scaffolds. Individual nucleotides are visible when zoomed in and colors are averaged in zoomed out images. Even in the absence of any annotation of a genome, FluentDNA allows the human eye to pick out key features of a genome assembly by size and nucleotide composition. With practice, major features of chromosome architecture including centromeres, isochores, telomeres, and tandem repeats can be identified from the naked sequence because changes in k-mer usage cause changes in color and texture. </p>
</div>
<div class="col-sm-4 offset-md-1 py-4">
<h4 class="text-white">Contact</h4>
<ul class="list-unstyled">
<li><a href="https://twitter.com/JosiahSeaman?s=20" class="text-white">Follow on Twitter</a></li>
<li><a href="https://www.researchgate.net/profile/Josiah_Seaman" class="text-white">Follow on Researchgate</a></li>
<li><a href="https://uk.linkedin.com/in/josiah-seaman-2557b3a" class="text-white">Follow on LinkedIn</a></li>
<li><a href="mailto:[email protected]" class="text-white">Email me</a></li>
</ul>
</div>
</div>
</div>
</div>
<div class="navbar navbar-dark bg-dark shadow-sm">
<div class="container d-flex justify-content-between">
<a href="#" class="navbar-brand d-flex align-items-center">
<strong>Josiah Seaman</strong>
</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarHeader"
aria-controls="navbarHeader" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
</div>
</div>
</header>
<main role="main">
<section class="jumbotron text-center">
<div class="container">
<h1>Fluent DNA</h1>
<p class="lead text-muted">Resources</p>
<p>
<a href="https://github.com/josiahseaman/FluentDNA/releases" class="btn btn-primary my-2">Download FluentDNA</a>
<a href="https://github.com/josiahseaman/FluentDNA" class="btn btn-secondary my-2">Source Code</a>
<a href="https://www.frontiersin.org/articles/10.3389/fgene.2020.00292/full" class="btn btn-secondary my-2">Technical Paper</a>
</p>
</div>
</section>
<div class="album py-5 bg-light">
<div class="container">
<h2>Visualizations from FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments</h2>
<p>These samples are listed in the <a href="https://www.frontiersin.org/articles/10.3389/fgene.2020.00292/full">Fluent DNA paper</a>.</p>
<div class="row">
<div class="col-md-4">
<div class="card mb-4 shadow-sm">
<a href="http://fluentdna.com/Human_Genome_Hg38_and_Genes_Gencodev30/">
<img src="img/FluentDNA/Human_Genome.png" width="350" height="400"
alt="Human Genome">
</a>
<div class="card-body">
<p class="card-text">Human Genome</p>
<div class="d-flex justify-content-between align-items-center">
<div class="btn-group">
<button type="button" class="btn btn-sm btn-outline-secondary">View</button>
<a href="https://fluentdna.com/Human_Genome_Hg38_and_Genes_Gencodev30.zip"
button type="button" class="btn btn-sm btn-outline-secondary">Download</button></a>
</div>
<small class="text-muted">.</small>
</div>
</div>
</div>
</div>
<div class="col-md-4">
<div class="card mb-4 shadow-sm">
<a href="http://fluentdna.com/Human_Hg38_chr18_vs_Chimpanzee_PanTro6_chr18/">
<img src="img/FluentDNA/Human_chr18_vs_Chimpanzee.png" width="350" height="400"
alt="Human vs Chimpanzee (chr 18)">
</a>
<div class="card-body">
<p class="card-text">Human vs Chimpanzee (chr 18)</p>
<div class="d-flex justify-content-between align-items-center">
<div class="btn-group">
<button type="button" class="btn btn-sm btn-outline-secondary">View</button>
<a href="https://fluentdna.com/Human%20Hg38%20chr18%20vs%20Chimpanzee%20PanTro6_chr18.zip"
button type="button" class="btn btn-sm btn-outline-secondary">Download</button></a>
</div>
<small class="text-muted">.</small>
</div>
</div>
</div>
</div>
<div class="col-md-4">
<div class="card mb-4 shadow-sm">
<a href="https://fluentdna.com/Human_Hg38_Chromosome_18_Repeats_-_alphabetical/">
<img src="img/FluentDNA/Human_Repeats_Chr18.png" width="350" height="400"
alt="Human Repeats (chr 18)">
</a>
<div class="card-body">
<p class="card-text">Human Repeats (chr 18)</p>
<div class="d-flex justify-content-between align-items-center">
<div class="btn-group">
<button type="button" class="btn btn-sm btn-outline-secondary">View</button>
<a href="https://fluentdna.com/Human%20Hg38%20Chromosome%2018%20Repeats%20-%20alphabetical.zip"
button type="button" class="btn btn-sm btn-outline-secondary">Download</button></a>
</div>
<small class="text-muted">.</small>
</div>
</div>
</div>
</div>
<div class="col-md-4">
<div class="card mb-4 shadow-sm">
<a href="https://fluentdna.com/Human_Genome_Hg38_chr18_with_Gencode_v30/">
<img src="img/FluentDNA/Human_chr18.png" width="350" height="400"
alt="Human (chr 18)">
</a>
<div class="card-body">
<p class="card-text">Human (chr 18)</p>
<div class="d-flex justify-content-between align-items-center">
<div class="btn-group">
<button type="button" class="btn btn-sm btn-outline-secondary">View</button>
<a href="https://fluentdna.com/Human_Genome_Hg38_chr18_with_Gencode_v30.zip"
button type="button" class="btn btn-sm btn-outline-secondary">Download</button></a>
</div>
<small class="text-muted">.</small>
</div>
</div>
</div>
</div>
<div class="col-md-4">
<div class="card mb-4 shadow-sm">
<a href="https://fluentdna.com/Human_Ideogram_Hg38_chr18_with_Gencode_v30/">
<img src="img/FluentDNA/Human_Ideogram_chr18.png" width="350"
height="400" alt="Human Ideogram (chr 18)">
</a>
<div class="card-body">
<p class="card-text">Human Ideogram (chr 18)</p>
<div class="d-flex justify-content-between align-items-center">
<div class="btn-group">
<button type="button" class="btn btn-sm btn-outline-secondary">View</button>
<a href="https://fluentdna.com/Human%20Ideogram%20Hg38%20chr18%20with%20Gencode%20v30.zip"
button type="button" class="btn btn-sm btn-outline-secondary">Download</button></a>
</div>
<small class="text-muted">.</small>
</div>
</div>
</div>
</div>
<div class="col-md-4">
<div class="card mb-4 shadow-sm">
<a href="https://fluentdna.com/Human_Hg38_vs_Chimpanzee_PanTro6/">
<img src="img/FluentDNA/Human_vs_Chimpanzee.png" width="350" height="400"
alt="Human vs Chimpanzee">
</a>
<div class="card-body">
<p class="card-text">Human vs Chimpanzee</p>
<div class="d-flex justify-content-between align-items-center">
<div class="btn-group">
<!--placeholder for buttons -->
</div>
<small class="text-muted">.</small>
</div>
</div>
</div>
</div>
<div class="col-md-4">
<div class="card mb-4 shadow-sm">
<a href="https://fluentdna.com/Unique_Human_Genes_and_Centromere_vs_Chimpanzee_PanTro6/">
<img src="img/FluentDNA/Unique_Human_Genes_and_Centromere_vs_Chimpanzee.png" width="350" height="400"
alt="Unique Human (Genes and Centromere) vs Chimpanzee">
</a>
<div class="card-body">
<p class="card-text">Unique Human (Genes and Centromere) vs Chimpanzee</p>
<div class="d-flex justify-content-between align-items-center">
<div class="btn-group">
<button type="button" class="btn btn-sm btn-outline-secondary">View</button>
<a href="https://fluentdna.com/Unique%20Human%20Genes%20and%20Centromere%20vs%20Chimpanzee%20PanTro6%20-%20packed2.zip">
<button type="button" class="btn btn-sm btn-outline-secondary">Download</button>
</a>
</div>
<small class="text-muted">.</small>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="album py-5 bg-light">
<div class="container">
<h2>More Samples </h2>
<p>These samples are not listed in the <a href="https://fluentdna.com">Fluent DNA</a> paper.</p>
<div class="row">
<div class="col-md-4">
<div class="card mb-4 shadow-sm">
<a href="https://fluentdna.com/Unique_Human_vs_Chimp_PanTro6_sequence_only/">
<img src="img/FluentDNA/Unique_Human_vs_Chimpanzee.png" width="350" height="400"
alt="Unique Human vs Chimpanzee">
</a>
<div class="card-body">
<p class="card-text">Unique Human vs Chimpanzee</p>
<div class="d-flex justify-content-between align-items-center">
<div class="btn-group">
<button type="button" class="btn btn-sm btn-outline-secondary">View</button>
<a href="https://fluentdna.com/Unique%20Human%20vs%20Chimp%20PanTro6.zip"
button type="button" class="btn btn-sm btn-outline-secondary">Download</button></a>
</div>
<small class="text-muted">.</small>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</main>
<footer class="text-muted">
<div class="container">
<p>Related project <a href="https://graph-genome.github.io">Pantograph - Pangenome Browser</a>.
</p>
</div>
</footer>
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