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| 1 | <!DOCTYPE html> |
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| 2 | <html lang="en"> |
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| 3 | |||
| 4 | <head> |
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| 5 | <!-- Google tag (gtag.js) --> |
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| 6 | <script async src="https://www.googletagmanager.com/gtag/js?id=G-0LTP0WK7EM"></script> |
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| 7 | <script> |
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| 8 | window.dataLayer = window.dataLayer || []; |
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| 9 | function gtag() { dataLayer.push(arguments); } |
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| 10 | gtag('js', new Date()); |
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| 11 | |||
| 12 | gtag('config', 'G-0LTP0WK7EM'); |
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| 13 | </script> |
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| 14 | <meta charset="UTF-8"> |
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| 15 | <meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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| 16 | <title>Documentation - DNAnalyzer</title> |
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| 17 | <meta name="description" |
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| 18 | content="Comprehensive documentation for DNAnalyzer - Get started with our powerful DNA analysis tools and learn how to use all features."> |
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| 19 | |||
| 20 | <!-- Stylesheets --> |
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| 21 | <link rel="stylesheet" href="../style.css"> |
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| 22 | <link rel="stylesheet" href="docs.css"> |
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| 23 | <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css"> |
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| 24 | <link rel="preconnect" href="https://fonts.googleapis.com"> |
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| 25 | <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin> |
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| 26 | <link |
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| 27 | href="https://fonts.googleapis.com/css2?family=Inter:wght@300;400;500;600;700&family=IBM+Plex+Mono:wght@400;500;600&display=swap" |
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| 28 | rel="stylesheet"> |
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| 29 | |||
| 30 | <!-- Favicon --> |
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| 31 | <link rel="shortcut icon" href="../assets/icons/Icon_Dark_BG.svg" type="image/svg+xml"> |
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| 32 | </head> |
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| 33 | |||
| 34 | <body> |
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| 35 | <!-- Background effects --> |
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| 36 | <div class="bg-gradient"> |
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| 37 | <div class="bg-blob bg-blob-1"></div> |
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| 38 | <div class="bg-blob bg-blob-2"></div> |
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| 39 | </div> |
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| 40 | |||
| 41 | <div class="notification-banner"> |
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| 42 | <span>Exclusive WSSEF Preview: </span> |
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| 43 | <span> Transformer Architecture in Epigenomics!</span> |
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| 44 | <a href="https://epiclassify.dnanalyzer.org" target="_blank" class="notification-link">Explore Now</a> |
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| 45 | <button class="notification-close" aria-label="Dismiss notification"></button> |
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| 46 | </div> |
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| 47 | |||
| 48 | <!-- Navbar --> |
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| 49 | <nav class="navbar" id="navbar"> |
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| 50 | <div class="container navbar-container"> |
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| 51 | <a href="../index.html" class="logo"> |
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| 52 | <img src="../assets/icons/Icon_Dark_BG.svg" alt="DNAnalyzer Logo"> |
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| 53 | <span class="logo-text">DNAnalyzer</span> |
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| 54 | </a> |
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| 55 | |||
| 56 | <button class="mobile-toggle" id="mobileToggle" aria-label="Toggle navigation"> |
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| 57 | <i class="fas fa-bars"></i> |
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| 58 | </button> |
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| 59 | |||
| 60 | <ul class="nav-links" id="navLinks"> |
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| 61 | <li><a href="../index.html">Home</a></li> |
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| 62 | <li><a href="../features/features.html">Features</a></li> |
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| 63 | <li><a href="../analyzer/analyzer.html">Analyzer</a></li> |
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| 64 | <li><a href="../server/server.html">Server</a></li> |
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| 65 | <li><a href="docs.html" class="active">Docs</a></li> |
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| 66 | <li><a href="../about/about.html">About</a></li> |
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| 67 | </ul> |
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| 68 | |||
| 69 | <div class="nav-buttons"> |
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| 70 | <a href="https://github.com/VerisimilitudeX/DNAnalyzer" class="btn btn-secondary btn-sm"> |
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| 71 | <i class="fab fa-github btn-icon"></i> GitHub |
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| 72 | </a> |
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| 73 | </div> |
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| 74 | </div> |
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| 75 | </nav> |
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| 76 | |||
| 77 | <!-- Documentation Layout --> |
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| 78 | <div class="docs-layout"> |
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| 79 | <!-- Sidebar (Left) --> |
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| 80 | <aside class="docs-sidebar" id="docsSidebar"> |
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| 81 | <div class="sidebar-header"> |
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| 82 | <h2>Documentation</h2> |
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| 83 | <button class="mobile-close" id="closeSidebar"> |
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| 84 | <i class="fas fa-times"></i> |
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| 85 | </button> |
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| 86 | </div> |
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| 87 | |||
| 88 | <div class="sidebar-search"> |
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| 89 | <div class="search-input-wrapper"> |
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| 90 | <i class="fas fa-search"></i> |
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| 91 | <input type="text" id="docsSearch" placeholder="Search documentation..."> |
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| 92 | </div> |
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| 93 | </div> |
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| 94 | |||
| 95 | <nav class="sidebar-nav"> |
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| 96 | <div class="nav-section"> |
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| 97 | <h3>Getting Started</h3> |
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| 98 | <ul> |
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| 99 | <li><a href="#introduction" class="active">Introduction</a></li> |
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| 100 | <li><a href="#installation">Installation</a></li> |
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| 101 | <li><a href="#quick-start">Quick Start</a></li> |
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| 102 | </ul> |
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| 103 | </div> |
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| 104 | |||
| 105 | <div class="nav-section"> |
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| 106 | <h3>Core Concepts</h3> |
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| 107 | <ul> |
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| 108 | <li><a href="#sequence-analysis">Sequence Analysis</a></li> |
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| 109 | <li><a href="#codon-detection">Codon Detection</a></li> |
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| 110 | <li><a href="#reading-frames">Reading Frames</a></li> |
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| 111 | <li><a href="#protein-prediction">Protein Prediction</a></li> |
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| 112 | </ul> |
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| 113 | </div> |
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| 114 | |||
| 115 | <div class="nav-section"> |
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| 116 | <h3>Advanced Usage</h3> |
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| 117 | <ul> |
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| 118 | <li><a href="#server-setup">Server Setup</a></li> |
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| 119 | <li><a href="#api-reference">API Reference</a></li> |
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| 120 | <li><a href="#cli-usage">CLI Usage</a></li> |
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| 121 | </ul> |
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| 122 | </div> |
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| 123 | |||
| 124 | <div class="nav-section"> |
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| 125 | <h3>Resources</h3> |
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| 126 | <ul> |
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| 127 | <li><a href="#faq">FAQ</a></li> |
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| 128 | <li><a href="#troubleshooting">Troubleshooting</a></li> |
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| 129 | <li><a href="#community">Community</a></li> |
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| 130 | </ul> |
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| 131 | </div> |
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| 132 | </nav> |
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| 133 | </aside> |
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| 134 | |||
| 135 | <!-- Content (Right) --> |
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| 136 | <div class="docs-content"> |
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| 137 | <div class="docs-mobile-header"> |
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| 138 | <button class="sidebar-toggle" id="sidebarToggle"> |
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| 139 | <i class="fas fa-bars"></i> |
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| 140 | </button> |
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| 141 | <h2>Documentation</h2> |
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| 142 | </div> |
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| 143 | |||
| 144 | <div class="docs-container"> |
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| 145 | <!-- Introduction --> |
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| 146 | <section id="introduction" class="doc-section"> |
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| 147 | <h1>Introduction to DNAnalyzer</h1> |
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| 148 | <p class="lead">DNAnalyzer is a powerful, privacy-focused DNA analysis tool using advanced machine |
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| 149 | learning models for accurate, on-device genomic analysis.</p> |
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| 150 | |||
| 151 | <p>This documentation will guide you through the installation, setup, and usage of DNAnalyzer for |
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| 152 | various DNA analysis tasks. Whether you're a researcher, educator, or bioinformatics enthusiast, |
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| 153 | you'll find comprehensive information on all of DNAnalyzer's capabilities.</p> |
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| 154 | |||
| 155 | <div class="info-box"> |
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| 156 | <h3>Key Features</h3> |
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| 157 | <ul> |
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| 158 | <li><strong>Privacy-First Analysis:</strong> All processing occurs on your device, ensuring |
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| 159 | your genetic data never leaves your system.</li> |
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| 160 | <li><strong>Machine Learning Powered:</strong> Advanced ML algorithms provide exceptional |
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| 161 | accuracy in sequence analysis.</li> |
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| 162 | <li><strong>Comprehensive Tools:</strong> From basic sequence statistics to advanced protein |
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| 163 | prediction and promoter detection.</li> |
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| 164 | <li><strong>Open Source:</strong> DNAnalyzer is completely open source under the MIT |
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| 165 | License.</li> |
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| 166 | </ul> |
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| 167 | </div> |
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| 168 | |||
| 169 | <h2>System Requirements</h2> |
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| 170 | <p>Before getting started, ensure your system meets the following requirements:</p> |
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| 171 | |||
| 172 | <div class="code-block"> |
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| 173 | <div class="code-header"> |
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| 174 | <span class="code-label">System Requirements</span> |
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| 175 | <button class="copy-button">Copy</button> |
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| 176 | </div> |
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| 177 | <pre><code>- Operating System: Windows 10+, macOS 10.14+, or Linux (Ubuntu 18.04+) |
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| 178 | - Memory: 2GB RAM minimum (4GB+ recommended for large sequences) |
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| 179 | - Storage: 200MB for application, additional space for sequence files |
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| 180 | - Browser: Chrome 80+, Firefox 75+, Safari 13+, Edge 80+ (for web interface) |
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| 181 | - Java Runtime: Java 17+ (for server mode)</code></pre> |
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| 182 | </div> |
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| 183 | </section> |
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| 184 | |||
| 185 | <!-- Installation --> |
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| 186 | <section id="installation" class="doc-section"> |
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| 187 | <h1>Installation</h1> |
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| 188 | <p>DNAnalyzer can be installed and used in multiple ways depending on your needs and technical |
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| 189 | preferences.</p> |
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| 190 | |||
| 191 | <h2>Web Interface (No Installation)</h2> |
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| 192 | <p>The simplest way to use DNAnalyzer is through our web interface, which requires no installation: |
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| 193 | </p> |
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| 194 | <ol> |
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| 195 | <li>Visit <a href="../analyzer/analyzer.html">DNAnalyzer Web App</a></li> |
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| 196 | <li>Upload your DNA sequence files</li> |
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| 197 | <li>Select analysis options and get results</li> |
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| 198 | </ol> |
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| 199 | <p>The web interface runs entirely in your browser, ensuring your data never leaves your device.</p> |
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| 200 | |||
| 201 | <h2>Local Server Installation</h2> |
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| 202 | <p>For more advanced usage or batch processing, you can install DNAnalyzer as a local server:</p> |
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| 203 | |||
| 204 | <div class="tabs"> |
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| 205 | <div class="tab-header"> |
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| 206 | <button class="tab-button active" data-tab="windows">Windows</button> |
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| 207 | <button class="tab-button" data-tab="macos">macOS</button> |
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| 208 | <button class="tab-button" data-tab="linux">Linux</button> |
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| 209 | </div> |
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| 210 | |||
| 211 | <div class="tab-content active" id="windows"> |
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| 212 | <ol> |
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| 213 | <li>Download the latest <a |
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| 214 | href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer |
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| 215 | release</a> for Windows</li> |
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| 216 | <li>Extract the ZIP file to your preferred location</li> |
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| 217 | <li>Ensure Java 17 or newer is installed on your system</li> |
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| 218 | <li>Double-click on <code>dnanalyzer.bat</code> to start the server</li> |
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| 219 | <li>Access the interface at <code>http://localhost:8080</code> in your browser</li> |
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| 220 | </ol> |
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| 221 | </div> |
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| 222 | |||
| 223 | <div class="tab-content" id="macos"> |
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| 224 | <ol> |
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| 225 | <li>Download the latest <a |
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| 226 | href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer |
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| 227 | release</a> for macOS</li> |
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| 228 | <li>Extract the ZIP file to your preferred location</li> |
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| 229 | <li>Ensure Java 17 or newer is installed on your system</li> |
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| 230 | <li>Open Terminal and navigate to the extracted folder</li> |
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| 231 | <li>Run <code>chmod +x dnanalyzer.sh</code> to make the script executable</li> |
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| 232 | <li>Execute <code>./dnanalyzer.sh</code> to start the server</li> |
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| 233 | <li>Access the interface at <code>http://localhost:8080</code> in your browser</li> |
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| 234 | </ol> |
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| 235 | </div> |
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| 236 | |||
| 237 | <div class="tab-content" id="linux"> |
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| 238 | <ol> |
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| 239 | <li>Download the latest <a |
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| 240 | href="https://github.com/VerisimilitudeX/DNAnalyzer/releases">DNAnalyzer |
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| 241 | release</a> for Linux</li> |
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| 242 | <li>Extract the archive to your preferred location</li> |
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| 243 | <li>Ensure Java 17 or newer is installed on your system</li> |
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| 244 | <li>Open Terminal and navigate to the extracted folder</li> |
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| 245 | <li>Run <code>chmod +x dnanalyzer.sh</code> to make the script executable</li> |
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| 246 | <li>Execute <code>./dnanalyzer.sh</code> to start the server</li> |
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| 247 | <li>Access the interface at <code>http://localhost:8080</code> in your browser</li> |
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| 248 | </ol> |
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| 249 | </div> |
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| 250 | </div> |
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| 251 | |||
| 252 | <h2>Building from Source</h2> |
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| 253 | <p>For developers or those who want the latest features, you can build DNAnalyzer from source:</p> |
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| 254 | |||
| 255 | <div class="code-block"> |
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| 256 | <div class="code-header"> |
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| 257 | <span class="code-label">Building from Source</span> |
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| 258 | <button class="copy-button">Copy</button> |
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| 259 | </div> |
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| 260 | <pre><code># Clone the repository |
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| 261 | git clone https://github.com/VerisimilitudeX/DNAnalyzer.git |
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| 262 | cd DNAnalyzer |
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| 263 | |||
| 264 | # Make the Gradle wrapper executable |
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| 265 | chmod +x ./gradlew |
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| 266 | |||
| 267 | # Build the project |
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| 268 | ./gradlew clean bootJar |
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| 269 | |||
| 270 | # Run the server |
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| 271 | java -jar build/libs/DNAnalyzer.jar</code></pre> |
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| 272 | </div> |
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| 273 | </section> |
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| 274 | |||
| 275 | <!-- Quick Start --> |
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| 276 | <section id="quick-start" class="doc-section"> |
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| 277 | <h1>Quick Start Guide</h1> |
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| 278 | <p>This guide will help you quickly get started with DNAnalyzer's basic features.</p> |
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| 279 | |||
| 280 | <h2>Analyzing Your First DNA Sequence</h2> |
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| 281 | <p>Follow these steps to perform your first DNA sequence analysis:</p> |
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| 282 | |||
| 283 | <div class="steps"> |
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| 284 | <div class="step"> |
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| 285 | <div class="step-number">1</div> |
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| 286 | <div class="step-content"> |
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| 287 | <h3>Upload a Sequence</h3> |
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| 288 | <p>Navigate to the <a href="../analyzer/analyzer.html">DNA Analyzer</a> page and upload |
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| 289 | your FASTA or FASTQ file by dragging it to the upload area or clicking to browse. |
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| 290 | </p> |
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| 291 | <p><strong>Don't have a sequence file?</strong> Click "Import Sample" to use a |
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| 292 | pre-loaded sample sequence.</p> |
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| 293 | </div> |
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| 294 | </div> |
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| 295 | |||
| 296 | <div class="step"> |
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| 297 | <div class="step-number">2</div> |
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| 298 | <div class="step-content"> |
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| 299 | <h3>Select Analysis Options</h3> |
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| 300 | <p>Choose which analysis features you want to run:</p> |
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| 301 | <ul> |
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| 302 | <li><strong>Basic Analysis:</strong> Sequence length, GC content, base composition |
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| 303 | </li> |
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| 304 | <li><strong>Codon Analysis:</strong> Start codons, stop codons, reading frames</li> |
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| 305 | <li><strong>Advanced Features:</strong> Coverage analysis, protein prediction, |
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| 306 | promoter detection</li> |
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| 307 | </ul> |
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| 308 | </div> |
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| 309 | </div> |
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| 310 | |||
| 311 | <div class="step"> |
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| 312 | <div class="step-number">3</div> |
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| 313 | <div class="step-content"> |
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| 314 | <h3>Run Analysis</h3> |
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| 315 | <p>Click the "Start Analysis" button to process your sequence. The analysis time depends |
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| 316 | on the sequence length and selected options.</p> |
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| 317 | </div> |
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| 318 | </div> |
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| 319 | |||
| 320 | <div class="step"> |
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| 321 | <div class="step-number">4</div> |
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| 322 | <div class="step-content"> |
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| 323 | <h3>Review Results</h3> |
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| 324 | <p>Examine the analysis results, which include visualizations, statistics, and detailed |
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| 325 | information about your sequence.</p> |
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| 326 | <p>You can export the results in JSON, CSV, or text format for further processing or |
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| 327 | documentation.</p> |
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| 328 | </div> |
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| 329 | </div> |
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| 330 | </div> |
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| 331 | |||
| 332 | <div class="info-box tip"> |
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| 333 | <h3>Pro Tip</h3> |
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| 334 | <p>For large sequences (>1MB), consider using the local server installation for better |
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| 335 | performance and additional analysis options.</p> |
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| 336 | </div> |
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| 337 | </section> |
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| 338 | |||
| 339 | <!-- Sequence Analysis --> |
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| 340 | <section id="sequence-analysis" class="doc-section"> |
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| 341 | <h1>Sequence Analysis</h1> |
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| 342 | <p>DNAnalyzer provides comprehensive tools to analyze the basic properties of DNA sequences.</p> |
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| 343 | |||
| 344 | <h2>Base Composition Analysis</h2> |
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| 345 | <p>One of the fundamental analyses is determining the nucleotide composition of your DNA sequence: |
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| 346 | </p> |
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| 347 | |||
| 348 | <ul> |
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| 349 | <li><strong>Nucleotide Counts:</strong> Total count of A, T, G, C, and any other bases (N) in |
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| 350 | the sequence</li> |
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| 351 | <li><strong>Percentage Distribution:</strong> Proportion of each nucleotide type</li> |
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| 352 | <li><strong>Visualization:</strong> Interactive bar chart showing the distribution</li> |
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| 353 | </ul> |
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| 354 | |||
| 355 | <h2>GC Content Analysis</h2> |
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| 356 | <p>GC content is the percentage of nitrogenous bases in a DNA molecule that are either guanine (G) |
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| 357 | or cytosine (C):</p> |
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| 358 | |||
| 359 | <div class="code-block"> |
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| 360 | <div class="code-header"> |
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| 361 | <span class="code-label">GC Content Formula</span> |
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| 362 | <button class="copy-button">Copy</button> |
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| 363 | </div> |
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| 364 | <pre><code>GC Content (%) = (G + C) / (A + T + G + C) × 100</code></pre> |
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| 365 | </div> |
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| 366 | |||
| 367 | <p>GC content is important because:</p> |
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| 368 | <ul> |
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| 369 | <li>It affects DNA stability (higher GC content = more stable)</li> |
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| 370 | <li>GC-rich regions often indicate regulatory elements and gene-dense areas</li> |
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| 371 | <li>Different organisms have characteristic GC content ranges</li> |
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| 372 | </ul> |
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| 373 | |||
| 374 | <div class="info-box"> |
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| 375 | <h3>Interpreting GC Content</h3> |
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| 376 | <ul> |
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| 377 | <li><strong>Low GC (< 40%):</strong> Common in AT-rich genomes like certain bacteria</li> |
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| 378 | <li><strong>Medium GC (40-60%):</strong> Typical of many eukaryotic genomes, including |
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| 379 | humans</li> |
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| 380 | <li><strong>High GC (> 60%):</strong> Often found in gene-rich regions and certain |
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| 381 | prokaryotes</li> |
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| 382 | </ul> |
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| 383 | </div> |
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| 384 | </section> |
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| 385 | |||
| 386 | <!-- More sections would continue here... --> |
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| 387 | |||
| 388 | <!-- API Reference --> |
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| 389 | <section id="api-reference" class="doc-section"> |
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| 390 | <h1>API Reference</h1> |
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| 391 | <p>DNAnalyzer provides a RESTful API when running in server mode, allowing programmatic access to |
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| 392 | all analysis features.</p> |
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| 393 | |||
| 394 | <h2>API Endpoints</h2> |
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| 395 | <p>The following endpoints are available when the server is running:</p> |
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| 396 | |||
| 397 | <div class="api-endpoint"> |
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| 398 | <div class="endpoint-method get">GET</div> |
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| 399 | <div class="endpoint-path">/api/v1/status</div> |
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| 400 | <div class="endpoint-description"> |
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| 401 | <p>Check server status and version information</p> |
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| 402 | <h4>Response</h4> |
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| 403 | <div class="code-block"> |
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| 404 | <pre><code>{ |
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| 405 | "status": "running", |
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| 406 | "version": "1.0.0", |
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| 407 | "uptime": "12h 34m 56s" |
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| 408 | }</code></pre> |
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| 409 | </div> |
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| 410 | </div> |
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| 411 | </div> |
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| 412 | |||
| 413 | <div class="api-endpoint"> |
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| 414 | <div class="endpoint-method post">POST</div> |
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| 415 | <div class="endpoint-path">/api/v1/analyze</div> |
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| 416 | <div class="endpoint-description"> |
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| 417 | <p>Analyze a DNA sequence file</p> |
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| 418 | <h4>Request</h4> |
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| 419 | <p>Form data with the following parameters:</p> |
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| 420 | <ul> |
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| 421 | <li><code>dnaFile</code> (required): The DNA sequence file to analyze</li> |
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| 422 | <li><code>options</code>: JSON string with analysis options</li> |
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| 423 | </ul> |
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| 424 | <h4>Response</h4> |
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| 425 | <div class="code-block"> |
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| 426 | <pre><code>{ |
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| 427 | "sequence": { |
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| 428 | "length": 1234, |
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| 429 | "filename": "example.fa" |
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| 430 | }, |
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| 431 | "basePairs": { |
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| 432 | "counts": { "A": 300, "T": 310, "G": 320, "C": 304 }, |
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| 433 | "percentages": { "A": 24.3, "T": 25.1, "G": 25.9, "C": 24.7 }, |
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| 434 | "gcContent": 50.6 |
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| 435 | }, |
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| 436 | "analysis": { |
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| 437 | // Additional analysis results based on options |
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| 438 | } |
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| 439 | }</code></pre> |
||
| 440 | </div> |
||
| 441 | </div> |
||
| 442 | </div> |
||
| 443 | |||
| 444 | <div class="api-endpoint"> |
||
| 445 | <div class="endpoint-method post">POST</div> |
||
| 446 | <div class="endpoint-path">/api/v1/base-pairs</div> |
||
| 447 | <div class="endpoint-description"> |
||
| 448 | <p>Analyze base pair composition of a DNA sequence</p> |
||
| 449 | <h4>Request</h4> |
||
| 450 | <div class="code-block"> |
||
| 451 | <pre><code>{ |
||
| 452 | "sequence": "ATGCATGCATGC" |
||
| 453 | }</code></pre> |
||
| 454 | </div> |
||
| 455 | <h4>Response</h4> |
||
| 456 | <div class="code-block"> |
||
| 457 | <pre><code>{ |
||
| 458 | "counts": { "A": 3, "T": 3, "G": 3, "C": 3 }, |
||
| 459 | "percentages": { "A": 25, "T": 25, "G": 25, "C": 25 }, |
||
| 460 | "gcContent": 50 |
||
| 461 | }</code></pre> |
||
| 462 | </div> |
||
| 463 | </div> |
||
| 464 | </div> |
||
| 465 | |||
| 466 | <h2>Python Client Example</h2> |
||
| 467 | <p>Here's a simple Python example to interact with the DNAnalyzer API:</p> |
||
| 468 | |||
| 469 | <div class="code-block"> |
||
| 470 | <div class="code-header"> |
||
| 471 | <span class="code-label">Python</span> |
||
| 472 | <button class="copy-button">Copy</button> |
||
| 473 | </div> |
||
| 474 | <pre><code>import requests |
||
| 475 | |||
| 476 | # API base URL |
||
| 477 | BASE_URL = "http://localhost:8080/api/v1" |
||
| 478 | |||
| 479 | # Check server status |
||
| 480 | response = requests.get(f"{BASE_URL}/status") |
||
| 481 | print("Server status:", response.json()) |
||
| 482 | |||
| 483 | # Analyze a sequence |
||
| 484 | with open("sequence.fa", "rb") as f: |
||
| 485 | files = {"dnaFile": f} |
||
| 486 | options = { |
||
| 487 | "sequence-length": True, |
||
| 488 | "gc-content": True, |
||
| 489 | "base-composition": True, |
||
| 490 | "start-codons": True, |
||
| 491 | "stop-codons": True |
||
| 492 | } |
||
| 493 | data = {"options": json.dumps(options)} |
||
| 494 | response = requests.post(f"{BASE_URL}/analyze", files=files, data=data) |
||
| 495 | |||
| 496 | # Print results |
||
| 497 | result = response.json() |
||
| 498 | print(f"Sequence length: {result['sequence']['length']}") |
||
| 499 | print(f"GC content: {result['basePairs']['gcContent']}%")</code></pre> |
||
| 500 | </div> |
||
| 501 | </section> |
||
| 502 | |||
| 503 | <!-- FAQ Section --> |
||
| 504 | <section id="faq" class="doc-section"> |
||
| 505 | <h1>Frequently Asked Questions</h1> |
||
| 506 | |||
| 507 | <div class="faq-item"> |
||
| 508 | <div class="faq-question"> |
||
| 509 | <h3>Is my DNA data secure when using DNAnalyzer?</h3> |
||
| 510 | <i class="fas fa-chevron-down"></i> |
||
| 511 | </div> |
||
| 512 | <div class="faq-answer"> |
||
| 513 | <p>Yes, DNAnalyzer is designed with privacy as a fundamental principle. All processing |
||
| 514 | occurs locally on your device, and your DNA sequence data never leaves your system. In |
||
| 515 | web mode, analysis runs directly in your browser, and in server mode, it runs only on |
||
| 516 | your local machine. We don't collect, store, or transmit any of your sequence data.</p> |
||
| 517 | </div> |
||
| 518 | </div> |
||
| 519 | |||
| 520 | <div class="faq-item"> |
||
| 521 | <div class="faq-question"> |
||
| 522 | <h3>What file formats does DNAnalyzer support?</h3> |
||
| 523 | <i class="fas fa-chevron-down"></i> |
||
| 524 | </div> |
||
| 525 | <div class="faq-answer"> |
||
| 526 | <p>DNAnalyzer supports the following file formats:</p> |
||
| 527 | <ul> |
||
| 528 | <li>FASTA (.fa, .fasta)</li> |
||
| 529 | <li>FASTQ (.fastq)</li> |
||
| 530 | <li>Plain text (.txt) containing DNA sequences</li> |
||
| 531 | </ul> |
||
| 532 | <p>The sequences should contain only A, T, G, C, and N (unknown) nucleotides. Other |
||
| 533 | characters will be treated as unknown bases.</p> |
||
| 534 | </div> |
||
| 535 | </div> |
||
| 536 | |||
| 537 | <div class="faq-item"> |
||
| 538 | <div class="faq-question"> |
||
| 539 | <h3>How large of a sequence can DNAnalyzer handle?</h3> |
||
| 540 | <i class="fas fa-chevron-down"></i> |
||
| 541 | </div> |
||
| 542 | <div class="faq-answer"> |
||
| 543 | <p>The size limitations depend on the mode of operation:</p> |
||
| 544 | <ul> |
||
| 545 | <li><strong>Web Interface:</strong> Up to around 5MB sequence files, depending on your |
||
| 546 | browser and device memory</li> |
||
| 547 | <li><strong>Local Server:</strong> Can handle much larger sequences, typically up to |
||
| 548 | several hundred MB</li> |
||
| 549 | </ul> |
||
| 550 | <p>For very large genomes (e.g., human genome), we recommend using the local server |
||
| 551 | installation with a machine that has at least 8GB of RAM.</p> |
||
| 552 | </div> |
||
| 553 | </div> |
||
| 554 | |||
| 555 | <div class="faq-item"> |
||
| 556 | <div class="faq-question"> |
||
| 557 | <h3>Can DNAnalyzer analyze my 23andMe or Ancestry DNA data?</h3> |
||
| 558 | <i class="fas fa-chevron-down"></i> |
||
| 559 | </div> |
||
| 560 | <div class="faq-answer"> |
||
| 561 | <p>Not directly in the current version. DNAnalyzer is designed to work with full DNA |
||
| 562 | sequences rather than SNP genotype data from consumer genetics services. However, we're |
||
| 563 | developing a feature to support genotype data analysis in an upcoming version.</p> |
||
| 564 | <p>If you have raw data from these services, you would need to convert it to a suitable |
||
| 565 | format before using it with DNAnalyzer.</p> |
||
| 566 | </div> |
||
| 567 | </div> |
||
| 568 | |||
| 569 | <div class="faq-item"> |
||
| 570 | <div class="faq-question"> |
||
| 571 | <h3>Is DNAnalyzer open source?</h3> |
||
| 572 | <i class="fas fa-chevron-down"></i> |
||
| 573 | </div> |
||
| 574 | <div class="faq-answer"> |
||
| 575 | <p>Yes, DNAnalyzer is completely open source under the MIT License. You can view, modify, |
||
| 576 | and contribute to the code on our <a |
||
| 577 | href="https://github.com/VerisimilitudeX/DNAnalyzer">GitHub repository</a>.</p> |
||
| 578 | </div> |
||
| 579 | </div> |
||
| 580 | </section> |
||
| 581 | |||
| 582 | <!-- Community Section --> |
||
| 583 | <section id="community" class="doc-section"> |
||
| 584 | <h1>Community & Support</h1> |
||
| 585 | <p>DNAnalyzer has an active community of users and developers. Here's how you can get involved and |
||
| 586 | find support.</p> |
||
| 587 | |||
| 588 | <h2>Getting Help</h2> |
||
| 589 | <p>If you need assistance with DNAnalyzer, there are several resources available:</p> |
||
| 590 | |||
| 591 | <div class="community-resources"> |
||
| 592 | <div class="resource-card"> |
||
| 593 | <i class="fab fa-discord"></i> |
||
| 594 | <h3>Discord Community</h3> |
||
| 595 | <p>Join our Discord server for real-time assistance and discussions about DNAnalyzer.</p> |
||
| 596 | <a href="https://discord.gg/xNpujz49gj" class="btn btn-secondary btn-sm">Join Discord</a> |
||
| 597 | </div> |
||
| 598 | |||
| 599 | <div class="resource-card"> |
||
| 600 | <i class="fab fa-github"></i> |
||
| 601 | <h3>GitHub Issues</h3> |
||
| 602 | <p>Report bugs or request features through our GitHub issue tracker.</p> |
||
| 603 | <a href="https://github.com/VerisimilitudeX/DNAnalyzer/issues" |
||
| 604 | class="btn btn-secondary btn-sm">GitHub Issues</a> |
||
| 605 | </div> |
||
| 606 | |||
| 607 | <div class="resource-card"> |
||
| 608 | <i class="fas fa-book"></i> |
||
| 609 | <h3>Documentation</h3> |
||
| 610 | <p>Browse comprehensive guides and tutorials in our documentation.</p> |
||
| 611 | <a href="docs.html" class="btn btn-secondary btn-sm">View Docs</a> |
||
| 612 | </div> |
||
| 613 | </div> |
||
| 614 | |||
| 615 | <h2>Contributing</h2> |
||
| 616 | <p>DNAnalyzer is an open-source project, and we welcome contributions from the community. There are |
||
| 617 | many ways to contribute:</p> |
||
| 618 | |||
| 619 | <ul> |
||
| 620 | <li><strong>Code Contributions:</strong> Help improve DNAnalyzer by fixing bugs or adding new |
||
| 621 | features</li> |
||
| 622 | <li><strong>Documentation:</strong> Improve our guides, tutorials, and API documentation</li> |
||
| 623 | <li><strong>Testing:</strong> Test DNAnalyzer and report issues or suggest improvements</li> |
||
| 624 | <li><strong>Translations:</strong> Help translate DNAnalyzer into different languages</li> |
||
| 625 | </ul> |
||
| 626 | |||
| 627 | <p>To get started with contributing, please read our <a |
||
| 628 | href="https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/CONTRIBUTING.md">contribution |
||
| 629 | guidelines</a>.</p> |
||
| 630 | |||
| 631 | <div class="info-box"> |
||
| 632 | <h3>Code of Conduct</h3> |
||
| 633 | <p>We're committed to providing a welcoming and inclusive environment for all contributors. |
||
| 634 | Please read and follow our <a |
||
| 635 | href="https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/CODE_OF_CONDUCT.md">Code |
||
| 636 | of Conduct</a>.</p> |
||
| 637 | </div> |
||
| 638 | </section> |
||
| 639 | </div> |
||
| 640 | </div> |
||
| 641 | </div> |
||
| 642 | |||
| 643 | <!-- Footer --> |
||
| 644 | <footer class="footer"> |
||
| 645 | <div class="container"> |
||
| 646 | <div class="footer-grid"> |
||
| 647 | <div class="footer-brand"> |
||
| 648 | <img src="../assets/icons/Icon_Dark_BG.svg" alt="DNAnalyzer Logo"> |
||
| 649 | <p>DNAnalyzer is a powerful, privacy-focused DNA analysis tool using cutting-edge machine learning |
||
| 650 | models for accurate, on-device genomic analysis.</p> |
||
| 651 | |||
| 652 | <div class="footer-social"> |
||
| 653 | <a href="https://www.twitter.com/DNAnalyzer_" class="social-link"> |
||
| 654 | <i class="fab fa-twitter"></i> |
||
| 655 | </a> |
||
| 656 | <a href="https://github.com/VerisimilitudeX/DNAnalyzer" class="social-link"> |
||
| 657 | <i class="fab fa-github"></i> |
||
| 658 | </a> |
||
| 659 | <a href="#" class="social-link"> |
||
| 660 | <i class="fab fa-twitter"></i> |
||
| 661 | </a> |
||
| 662 | </div> |
||
| 663 | </div> |
||
| 664 | |||
| 665 | <div class="footer-nav"> |
||
| 666 | <h4>Product</h4> |
||
| 667 | <ul> |
||
| 668 | <li><a href="../features/features.html">Features</a></li> |
||
| 669 | <li><a href="../analyzer/analyzer.html">DNA Analyzer</a></li> |
||
| 670 | <li><a href="../server/server.html">Server</a></li> |
||
| 671 | <li><a href="docs.html">Documentation</a></li> |
||
| 672 | </ul> |
||
| 673 | </div> |
||
| 674 | |||
| 675 | <div class="footer-nav"> |
||
| 676 | <h4>Resources</h4> |
||
| 677 | <ul> |
||
| 678 | <li><a href="getting-started.md">Getting Started</a></li> |
||
| 679 | <li><a href="citations.md">Citations</a></li> |
||
| 680 | <li><a href="research/genes.md">Gene Research</a></li> |
||
| 681 | <li><a href="samples/cli-arguments-examples.md">CLI Examples</a></li> |
||
| 682 | </ul> |
||
| 683 | </div> |
||
| 684 | |||
| 685 | <div class="footer-nav"> |
||
| 686 | <h4>Community</h4> |
||
| 687 | <ul> |
||
| 688 | <li><a href="https://github.com/VerisimilitudeX/DNAnalyzer">GitHub</a></li> |
||
| 689 | <li><a href="https://discord.gg/xNpujz49gj">Discord</a></li> |
||
| 690 | <li><a href="contributing/CONTRIBUTING.md">Contributing</a></li> |
||
| 691 | <li><a href="../CODE_OF_CONDUCT.md">Code of Conduct</a></li> |
||
| 692 | </ul> |
||
| 693 | </div> |
||
| 694 | </div> |
||
| 695 | |||
| 696 | <div class="footer-bottom"> |
||
| 697 | <div class="footer-copyright"> |
||
| 698 | Copyright © Piyush Acharya 2025. DNAnalyzer is a fiscally sponsored 501(c)(3) nonprofit (EIN: |
||
| 699 | 81-2908499). MIT License. |
||
| 700 | </div> |
||
| 701 | |||
| 702 | <div class="footer-links"> |
||
| 703 | <a href="../LICENSE.md">License</a> |
||
| 704 | <a href="../SECURITY.md">Security</a> |
||
| 705 | <a href="../CITATION.cff">Citation</a> |
||
| 706 | </div> |
||
| 707 | </div> |
||
| 708 | </div> |
||
| 709 | </footer> |
||
| 710 | |||
| 711 | <!-- JavaScript --> |
||
| 712 | <script src="docs.js"></script> |
||
| 713 | </body> |
||
| 714 | |||
| 715 | </html> |