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<!DOCTYPE html>
<html lang="en">
<head>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-0LTP0WK7EM"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag() { dataLayer.push(arguments); }
gtag('js', new Date());
gtag('config', 'G-0LTP0WK7EM');
</script>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>DNA Analyzer - DNAnalyzer</title>
<meta name="description"
content="Analyze DNA sequences with advanced ML-powered tools. Upload FASTA or FASTQ files and get comprehensive analysis.">
<!-- Stylesheets -->
<link rel="stylesheet" href="../style.css">
<link rel="stylesheet" href="analyzer.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css">
<link rel="preconnect" href="https://fonts.googleapis.com">
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href="https://fonts.googleapis.com/css2?family=Inter:wght@300;400;500;600;700&family=IBM+Plex+Mono:wght@400;500;600&display=swap"
rel="stylesheet">
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<link rel="shortcut icon" href="../assets/icons/Icon_Dark_BG.svg" type="image/svg+xml">
</head>
<body>
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<div class="bg-gradient">
<div class="bg-blob bg-blob-1"></div>
<div class="bg-blob bg-blob-2"></div>
</div>
<div class="notification-banner">
<span>Exclusive WSSEF Preview: </span>
<span>&nbsp;Transformer Architecture in Epigenomics!</span>
<a href="https://epiclassify.dnanalyzer.org" target="_blank" class="notification-link">Explore Now</a>
<button class="notification-close" aria-label="Dismiss notification"></button>
</div>
<!-- Navbar -->
<nav class="navbar" id="navbar">
<div class="container navbar-container">
<a href="../index.html" class="logo">
<img src="../assets/icons/Icon_Dark_BG.svg" alt="DNAnalyzer Logo">
<span class="logo-text">DNAnalyzer</span>
</a>
<button class="mobile-toggle" id="mobileToggle" aria-label="Toggle navigation">
<i class="fas fa-bars"></i>
</button>
<ul class="nav-links" id="navLinks">
<li><a href="../index.html">Home</a></li>
<li><a href="../features/features.html">Features</a></li>
<li><a href="analyzer.html" class="active">Analyzer</a></li>
<li><a href="../server/server.html">Server</a></li>
<li><a href="../docs/docs.html">Docs</a></li>
<li><a href="../about/about.html">About</a></li>
</ul>
<div class="nav-buttons">
<a href="https://github.com/VerisimilitudeX/DNAnalyzer" class="btn btn-secondary btn-sm">
<i class="fab fa-github btn-icon"></i> GitHub
</a>
</div>
</div>
</nav>
<!-- Main Content -->
<main class="analyzer-main">
<div class="container">
<div class="analyzer-header">
<h1>DNA Sequence <span class="gradient-text">Analysis</span></h1>
<p>Analyze DNA sequences with advanced machine learning tools</p>
</div>
<div class="analyzer-dashboard">
<div class="dashboard-sidebar">
<div class="sidebar-section">
<h3>Analysis History</h3>
<div class="history-list" id="historyList">
<div class="history-empty">
<i class="fas fa-history"></i>
<p>No recent analyses</p>
</div>
</div>
</div>
<div class="sidebar-section">
<h3>Quick Actions</h3>
<div class="quick-actions">
<button id="importSampleBtn" class="sidebar-btn">
<i class="fas fa-file-import"></i>
Import Sample
</button>
<button id="clearOptionsBtn" class="sidebar-btn">
<i class="fas fa-undo"></i>
Reset Options
</button>
<button id="helpBtn" class="sidebar-btn">
<i class="fas fa-question-circle"></i>
Help Guide
</button>
</div>
</div>
<div class="sidebar-section api-status-container">
<h3>API Status</h3>
<div class="api-status" id="apiStatus">
<div class="status-indicator">
<div class="status-dot pulse"></div>
<span>Checking connection...</span>
</div>
</div>
</div>
</div>
<div class="dashboard-content">
<div class="analyzer-tabs">
<button class="tab-btn active" data-tab="dna-analysis">
<i class="fas fa-dna"></i>
DNA Analysis
</button>
<button class="tab-btn" data-tab="genetic-testing">
<i class="fas fa-vial"></i>
Genetic Testing
</button>
<button class="tab-btn" data-tab="batch-processing">
<i class="fas fa-layer-group"></i>
Batch Processing
</button>
</div>
<div class="tab-content active" id="dna-analysis">
<div class="analyzer-upload" id="fileDropZone">
<i class="fas fa-cloud-upload-alt"></i>
<h3>Upload DNA Sequence</h3>
<p>Drag and drop your sequence file here or click to browse</p>
<input type="file" id="fileInput" accept=".fa,.fasta,.fastq,.txt" hidden>
<span class="upload-formats">Supported formats: .fa, .fasta, .fastq, .txt</span>
</div>
<div class="analysis-options">
<h3>Analysis Options</h3>
<div class="options-grid">
<div class="option-card">
<div class="option-header">
<i class="fas fa-microscope"></i>
<h4>Basic Analysis</h4>
</div>
<div class="option-content">
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="sequence-length"
checked>
<span class="checkmark"></span>
Sequence Length
</label>
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="gc-content" checked>
<span class="checkmark"></span>
GC Content
</label>
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="base-composition"
checked>
<span class="checkmark"></span>
Base Composition
</label>
</div>
</div>
<div class="option-card">
<div class="option-header">
<i class="fas fa-dna"></i>
<h4>Codon Analysis</h4>
</div>
<div class="option-content">
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="start-codons" checked>
<span class="checkmark"></span>
Start Codons
</label>
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="stop-codons" checked>
<span class="checkmark"></span>
Stop Codons
</label>
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="reading-frames">
<span class="checkmark"></span>
Reading Frames
</label>
</div>
</div>
<div class="option-card">
<div class="option-header">
<i class="fas fa-chart-line"></i>
<h4>Advanced Features</h4>
</div>
<div class="option-content">
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="coverage">
<span class="checkmark"></span>
Coverage Analysis
</label>
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="protein-prediction">
<span class="checkmark"></span>
Protein Prediction
</label>
<label class="option-checkbox">
<input type="checkbox" name="analysis-option" value="promoter-detection">
<span class="checkmark"></span>
Promoter Detection
</label>
</div>
</div>
</div>
<button class="btn btn-primary analyze-btn" id="analyzeBtn" disabled>
<i class="fas fa-play"></i>
Start Analysis
</button>
</div>
</div>
<div class="tab-content" id="genetic-testing">
<div class="genetic-testing-container">
<div id="dropZone" class="drop-zone">
<i class="fas fa-dna"></i>
<h3>Upload DNA File or Drop Here</h3>
<p>Supported formats: .fastq, .fasta, .sam, .bam, .vcf</p>
<input type="file" id="dnaFileInput" accept=".fastq,.fasta,.sam,.bam,.vcf" />
<div class="sample-selector">
<p>Or try with a sample file:</p>
<select id="sampleFileSelect">
<option value="">Select a sample file...</option>
</select>
</div>
</div>
<div id="sequenceDisplay" class="sequence-display"></div>
<button id="analyzeButton" class="analyze-btn">
<i class="fas fa-microscope"></i>
Analyze DNA
</button>
<div id="loadingSpinner" class="loading-spinner" style="display: none;">
<div class="spinner"></div>
<p>Analyzing DNA sequence...</p>
</div>
<div id="errorDisplay" class="error-display"></div>
<div id="resultsContainer" class="results-container"></div>
</div>
</div>
<div class="tab-content" id="batch-processing">
<div class="coming-soon">
<i class="fas fa-layer-group"></i>
<h3>Batch Processing Coming Soon</h3>
<p>Process multiple DNA sequence files simultaneously for high-throughput analysis. Sign up
for our newsletter to be notified when this feature launches.</p>
</div>
</div>
</div>
</div>
<!-- Results Section (initially hidden) -->
<div class="analyzer-results" id="resultsSection" style="display: none;">
<div class="results-header">
<h2>Analysis Results</h2>
<div class="results-actions">
<div class="results-file-info" id="resultsFileInfo">
<i class="fas fa-file-alt"></i>
<span>sample.fa</span>
</div>
<button class="btn btn-secondary" id="exportBtn">
<i class="fas fa-download"></i>
Export Results
</button>
</div>
</div>
<div class="results-content" id="resultsContent">
<!-- Results will be inserted here by JavaScript -->
</div>
</div>
</div>
<!-- Export Modal -->
<div class="modal" id="exportModal">
<div class="modal-content">
<div class="modal-header">
<h3>Export Results</h3>
<button class="close-modal" id="closeExportModal">&times;</button>
</div>
<div class="modal-body">
<p>Choose format to download your analysis results:</p>
<div class="export-options">
<button class="export-option" data-format="json">
<i class="fas fa-file-code"></i>
<span>JSON</span>
</button>
<button class="export-option" data-format="csv">
<i class="fas fa-file-csv"></i>
<span>CSV</span>
</button>
<button class="export-option" data-format="txt">
<i class="fas fa-file-alt"></i>
<span>Text</span>
</button>
</div>
</div>
</div>
</div>
<!-- Help Modal -->
<div class="modal" id="helpModal">
<div class="modal-content">
<div class="modal-header">
<h3>DNA Analyzer Help</h3>
<button class="close-modal" id="closeHelpModal">&times;</button>
</div>
<div class="modal-body">
<h4>Getting Started</h4>
<p>To analyze DNA sequences, follow these steps:</p>
<ol>
<li>Upload a DNA sequence file (.fa, .fasta, .fastq, .txt) by dragging it to the upload area or
clicking to browse.</li>
<li>Select the analysis options you want to run on your sequence.</li>
<li>Click "Start Analysis" to process your sequence.</li>
<li>View the results and download them if needed.</li>
</ol>
<h4>Analysis Options</h4>
<p>DNAnalyzer offers several types of analysis:</p>
<ul>
<li><strong>Basic Analysis:</strong> Calculates sequence length, GC content percentage, and
nucleotide composition.</li>
<li><strong>Codon Analysis:</strong> Identifies start codons (ATG), stop codons (TAA, TAG, TGA),
and reading frames.</li>
<li><strong>Advanced Features:</strong> Performs coverage analysis, protein prediction, and
promoter sequence detection.</li>
</ul>
<h4>Need More Help?</h4>
<p>Check out our <a href="../docs/docs.html">Documentation</a> for detailed guides or join our <a
href="https://discord.gg/xNpujz49gj">Discord community</a> for support.</p>
</div>
</div>
</div>
</main>
<!-- Notification container -->
<div class="notification-container" id="notificationContainer"></div>
<!-- Footer -->
<footer class="footer">
<div class="container">
<div class="footer-grid">
<div class="footer-brand">
<img src="../assets/icons/Icon_Dark_BG.svg" alt="DNAnalyzer Logo">
<p>DNAnalyzer is a powerful, privacy-focused DNA analysis tool using cutting-edge machine learning
models for accurate, on-device genomic analysis.</p>
<div class="social-links">
<a href="https://github.com/VerisimilitudeX/DNAnalyzer" class="social-link">
<i class="fab fa-github"></i>
</a>
<a href="https://discord.gg/xNpujz49gj" class="social-link">
<i class="fab fa-discord"></i>
</a>
<a href="https://twitter.com/DNAnalyzer_" class="social-link">
<i class="fab fa-twitter"></i>
</a>
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d="M389.2 48h70.6L305.6 224.2 487 464H345L233.7 318.6 106.5 464H35.8L200.7 275.5 26.8 48H172.4L272.9 180.9 389.2 48zM364.4 421.8h39.1L151.1 88h-42L364.4 421.8z" />
</svg>
</a>
</div>
</div>
<div class="footer-nav">
<h4>Product</h4>
<ul>
<li><a href="../features/features.html">Features</a></li>
<li><a href="analyzer.html">DNA Analyzer</a></li>
<li><a href="../server/server.html">Server</a></li>
<li><a href="../docs/docs.html">Documentation</a></li>
</ul>
</div>
<div class="footer-nav">
<h4>Resources</h4>
<ul>
<li><a href="../docs/getting-started.md">Getting Started</a></li>
<li><a href="../docs/citations.md">Citations</a></li>
<li><a href="../docs/research/genes.md">Gene Research</a></li>
<li><a href="../docs/samples/cli-arguments-examples.md">CLI Examples</a></li>
</ul>
</div>
<div class="footer-nav">
<h4>Community</h4>
<ul>
<li><a href="https://github.com/VerisimilitudeX/DNAnalyzer">GitHub</a></li>
<li><a href="https://discord.gg/xNpujz49gj">Discord</a></li>
<li><a href="../docs/contributing/CONTRIBUTING.md">Contributing</a></li>
<li><a href="../CODE_OF_CONDUCT.md">Code of Conduct</a></li>
</ul>
</div>
</div>
<div class="footer-bottom">
<div class="footer-copyright">
Copyright &copy; Piyush Acharya 2025. DNAnalyzer is a fiscally sponsored 501(c)(3) nonprofit (EIN:
81-2908499). MIT License.
</div>
<div class="footer-links">
<a href="../LICENSE.md">License</a>
<a href="../SECURITY.md">Security</a>
<a href="../CITATION.cff">Citation</a>
</div>
</div>
</div>
</footer>
<!-- JavaScript -->
<script src="../assets/js/api-client.js"></script>
<script src="analyzer.js"></script>
<!-- Chart.js for visualizations -->
<script src="https://cdn.jsdelivr.net/npm/chart.js@3.7.1/dist/chart.min.js"></script>
<!-- Genetic Testing Script -->
<script src="genetic-testing.js"></script>
</body>
</html>