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--- a +++ b/web/features/features.html @@ -0,0 +1,637 @@ +<!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>Features - DNAnalyzer</title> + <meta name="description" + content="Explore DNAnalyzer's advanced features for DNA sequence analysis, including codon detection, high coverage analysis, and more."> + + <!-- Stylesheets --> + <link rel="stylesheet" href="../style.css"> + <link rel="stylesheet" href="features.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"> + <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin> + <link + 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"> + + <!-- Favicon --> + <link rel="shortcut icon" href="../assets/icons/Icon_Dark_BG.svg" type="image/svg+xml"> +</head> + +<body> + <!-- Background effects --> + <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> 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.html" class="active">Features</a></li> + <li><a href="../analyzer/analyzer.html">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> + <section class="features-hero"> + <div class="container"> + <div class="features-hero-content"> + <h1>DNAnalyzer <span class="gradient-text">Features</span></h1> + <p>Advanced DNA analysis capabilities powered by machine learning, designed for researchers, + educators, and enthusiasts.</p> + </div> + </div> + </section> + + <section class="section feature-highlights"> + <div class="container"> + <div class="section-title"> + <h2>Key Capabilities</h2> + <p>Our comprehensive suite of DNA analysis tools provides insights from basic sequence statistics to + advanced protein prediction</p> + </div> + + <div class="features-grid"> + <div class="feature-card" data-aos="fade-up"> + <div class="feature-icon"> + <i class="fas fa-microscope"></i> + </div> + <h3>Sequence Analysis</h3> + <p>Get detailed statistics about your DNA sequence, including length, GC content, and nucleotide + composition with intuitive visualizations.</p> + <a href="#sequence-analysis" class="feature-link">Learn more <i + class="fas fa-arrow-right"></i></a> + </div> + + <div class="feature-card" data-aos="fade-up" data-aos-delay="100"> + <div class="feature-icon"> + <i class="fas fa-dna"></i> + </div> + <h3>Codon Detection</h3> + <p>Identify start and stop codons across your sequence to locate potential protein-coding + regions with high precision.</p> + <a href="#codon-detection" class="feature-link">Learn more <i + class="fas fa-arrow-right"></i></a> + </div> + + <div class="feature-card" data-aos="fade-up" data-aos-delay="200"> + <div class="feature-icon"> + <i class="fas fa-project-diagram"></i> + </div> + <h3>Reading Frames</h3> + <p>Analyze all six reading frames to identify potential protein-coding regions and open reading + frames (ORFs).</p> + <a href="#reading-frames" class="feature-link">Learn more <i class="fas fa-arrow-right"></i></a> + </div> + + <div class="feature-card" data-aos="fade-up"> + <div class="feature-icon"> + <i class="fas fa-chart-bar"></i> + </div> + <h3>Coverage Analysis</h3> + <p>Identify high-coverage (GC-rich) regions, often associated with gene-dense areas and promoter + regions.</p> + <a href="#coverage-analysis" class="feature-link">Learn more <i + class="fas fa-arrow-right"></i></a> + </div> + + <div class="feature-card" data-aos="fade-up" data-aos-delay="100"> + <div class="feature-icon"> + <i class="fas fa-prescription"></i> + </div> + <h3>Protein Prediction</h3> + <p>Predict potential proteins from your DNA sequence and analyze their amino acid composition. + </p> + <a href="#protein-prediction" class="feature-link">Learn more <i + class="fas fa-arrow-right"></i></a> + </div> + + <div class="feature-card" data-aos="fade-up" data-aos-delay="200"> + <div class="feature-icon"> + <i class="fas fa-server"></i> + </div> + <h3>Local Server</h3> + <p>Deploy DNAnalyzer as a local server for secure, high-throughput analysis of sensitive genomic + data.</p> + <a href="#local-server" class="feature-link">Learn more <i class="fas fa-arrow-right"></i></a> + </div> + </div> + </div> + </section> + + <section id="sequence-analysis" class="section section-detailed feature-section-odd"> + <div class="container"> + <div class="feature-detailed"> + <div class="feature-image" data-aos="fade-right"> + <div class="feature-image-wrapper"> + <img src="../assets/screenshots/sequence-analysis.png" alt="Sequence Analysis" + onerror="this.src='../assets/icons/Icon_Dark_BG.svg'"> + </div> + </div> + <div class="feature-content" data-aos="fade-left"> + <h2>Sequence Analysis</h2> + <p>Our basic sequence analysis tools give you immediate insights into your DNA sequence + properties.</p> + + <ul class="feature-list"> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Base Composition</h4> + <p>Interactive visualization of nucleotide distribution with precise percentages</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>GC Content Calculation</h4> + <p>Identify regions with high GC content, important for gene density and stability + </p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Sequence Length Analysis</h4> + <p>Get exact measurements of your DNA sequence with support for very large genomes + </p> + </div> + </li> + </ul> + + <a href="../analyzer/analyzer.html" class="btn btn-primary">Try Sequence Analysis</a> + </div> + </div> + </div> + </section> + + <section id="codon-detection" class="section section-detailed feature-section-even"> + <div class="container"> + <div class="feature-detailed reverse"> + <div class="feature-image" data-aos="fade-left"> + <div class="feature-image-wrapper"> + <img src="../assets/screenshots/codon-detection.png" alt="Codon Detection" + onerror="this.src='../assets/icons/Icon_Dark_BG.svg'"> + </div> + </div> + <div class="feature-content" data-aos="fade-right"> + <h2>Codon Detection</h2> + <p>Identify critical codon patterns in your DNA sequence with our advanced detection algorithms. + </p> + + <ul class="feature-list"> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Start Codon Identification</h4> + <p>Automatically detect ATG start codons that initiate protein translation</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Stop Codon Recognition</h4> + <p>Find all TAA, TAG, and TGA stop codons that terminate protein synthesis</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Codon Frequency Analysis</h4> + <p>Analyze codon usage patterns across your sequence to identify potential gene + regions</p> + </div> + </li> + </ul> + + <a href="../analyzer/analyzer.html" class="btn btn-primary">Try Codon Detection</a> + </div> + </div> + </div> + </section> + + <section id="reading-frames" class="section section-detailed feature-section-odd"> + <div class="container"> + <div class="feature-detailed"> + <div class="feature-image" data-aos="fade-right"> + <div class="feature-image-wrapper"> + <img src="../assets/screenshots/reading-frames.png" alt="Reading Frames" + onerror="this.src='../assets/icons/Icon_Dark_BG.svg'"> + </div> + </div> + <div class="feature-content" data-aos="fade-left"> + <h2>Reading Frames Analysis</h2> + <p>Comprehensive analysis of all six reading frames to identify potential genes and coding + regions.</p> + + <ul class="feature-list"> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Six-Frame Translation</h4> + <p>Analyze three forward and three reverse reading frames simultaneously</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Open Reading Frame (ORF) Detection</h4> + <p>Identify complete ORFs from start to stop codons across all frames</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Gene Prediction</h4> + <p>Find potential genes based on ORF length and composition characteristics</p> + </div> + </li> + </ul> + + <a href="../analyzer/analyzer.html" class="btn btn-primary">Try Reading Frames Analysis</a> + </div> + </div> + </div> + </section> + + <section id="coverage-analysis" class="section section-detailed feature-section-even"> + <div class="container"> + <div class="feature-detailed reverse"> + <div class="feature-image" data-aos="fade-left"> + <div class="feature-image-wrapper"> + <img src="../assets/screenshots/coverage-analysis.png" alt="Coverage Analysis" + onerror="this.src='../assets/icons/Icon_Dark_BG.svg'"> + </div> + </div> + <div class="feature-content" data-aos="fade-right"> + <h2>Coverage Analysis</h2> + <p>Identify regions of interest with our powerful coverage analysis tools to spot regulatory + elements and gene-dense areas.</p> + + <ul class="feature-list"> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>GC-Rich Region Detection</h4> + <p>Find CpG islands and GC-rich regions often associated with gene promoters</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Promoter Element Identification</h4> + <p>Detect TATA boxes, BRE, INR, and DPE motifs that indicate promoter regions</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Visualization Tools</h4> + <p>Graphical representation of coverage across your sequence for easy interpretation + </p> + </div> + </li> + </ul> + + <a href="../analyzer/analyzer.html" class="btn btn-primary">Try Coverage Analysis</a> + </div> + </div> + </div> + </section> + + <section id="protein-prediction" class="section section-detailed feature-section-odd"> + <div class="container"> + <div class="feature-detailed"> + <div class="feature-image" data-aos="fade-right"> + <div class="feature-image-wrapper"> + <img src="../assets/screenshots/protein-prediction.png" alt="Protein Prediction" + onerror="this.src='../assets/icons/Icon_Dark_BG.svg'"> + </div> + </div> + <div class="feature-content" data-aos="fade-left"> + <h2>Protein Prediction</h2> + <p>Translate DNA sequences into proteins and analyze their properties with our advanced + prediction tools.</p> + + <ul class="feature-list"> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>ORF Translation</h4> + <p>Convert open reading frames to amino acid sequences using the standard genetic + code</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Protein Length Filtering</h4> + <p>Focus on proteins of significant length to identify functional gene products</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Amino Acid Composition</h4> + <p>Analyze the distribution of amino acids within predicted proteins</p> + </div> + </li> + </ul> + + <a href="../analyzer/analyzer.html" class="btn btn-primary">Try Protein Prediction</a> + </div> + </div> + </div> + </section> + + <section id="local-server" class="section section-detailed feature-section-even"> + <div class="container"> + <div class="feature-detailed reverse"> + <div class="feature-image" data-aos="fade-left"> + <div class="feature-image-wrapper"> + <img src="../assets/screenshots/local-server.png" alt="Local Server" + onerror="this.src='../assets/icons/Icon_Dark_BG.svg'"> + </div> + </div> + <div class="feature-content" data-aos="fade-right"> + <h2>Local Server Deployment</h2> + <p>Run DNAnalyzer as a local server for secure, high-throughput analysis of sensitive genomic + data.</p> + + <ul class="feature-list"> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>Privacy-Focused Analysis</h4> + <p>Keep sensitive genetic data on your own infrastructure with no external data + transfer</p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>High-Performance Processing</h4> + <p>Optimized for multi-core systems to handle large datasets and batch processing + </p> + </div> + </li> + <li> + <i class="fas fa-check-circle"></i> + <div> + <h4>API Integration</h4> + <p>RESTful API for seamless integration with your existing bioinformatics pipelines + </p> + </div> + </li> + </ul> + + <a href="../server/server.html" class="btn btn-primary">Learn About Server Setup</a> + </div> + </div> + </div> + </section> + + <section class="section comparison-section"> + <div class="container"> + <div class="section-title"> + <h2>Why Choose DNAnalyzer?</h2> + <p>See how DNAnalyzer compares to traditional DNA analysis tools</p> + </div> + + <div class="comparison-table-container" data-aos="fade-up"> + <table class="comparison-table"> + <thead> + <tr> + <th>Feature</th> + <th>DNAnalyzer</th> + <th>Traditional Tools</th> + </tr> + </thead> + <tbody> + <tr> + <td>User Interface</td> + <td><i class="fas fa-check-circle check-icon"></i> Modern web interface</td> + <td><i class="fas fa-times-circle x-icon"></i> Often command-line only</td> + </tr> + <tr> + <td>Privacy</td> + <td><i class="fas fa-check-circle check-icon"></i> On-device processing</td> + <td><i class="fas fa-times-circle x-icon"></i> May require server upload</td> + </tr> + <tr> + <td>Machine Learning</td> + <td><i class="fas fa-check-circle check-icon"></i> Advanced ML algorithms</td> + <td><i class="fas fa-times-circle x-icon"></i> Often rule-based only</td> + </tr> + <tr> + <td>Setup Complexity</td> + <td><i class="fas fa-check-circle check-icon"></i> Simple, instant setup</td> + <td><i class="fas fa-times-circle x-icon"></i> Complex dependencies</td> + </tr> + <tr> + <td>Visualization</td> + <td><i class="fas fa-check-circle check-icon"></i> Interactive graphics</td> + <td><i class="fas fa-times-circle x-icon"></i> Often text-only output</td> + </tr> + <tr> + <td>Multiple File Support</td> + <td><i class="fas fa-check-circle check-icon"></i> FASTA, FASTQ, plain text</td> + <td><i class="fas fa-check-circle check-icon"></i> Various formats</td> + </tr> + <tr> + <td>Cost</td> + <td><i class="fas fa-check-circle check-icon"></i> Free, open-source</td> + <td><i class="fas fa-minus-circle minus-icon"></i> Often commercial</td> + </tr> + </tbody> + </table> + </div> + </div> + </section> + + <section class="section testimonials-section"> + <div class="container"> + <div class="section-title"> + <h2>What Our Users Say</h2> + <p>Hear from researchers and educators who use DNAnalyzer</p> + </div> + + <div class="testimonials-grid"> + <div class="testimonial-card" data-aos="fade-up"> + <div class="testimonial-content"> + <p>"DNAnalyzer has transformed how I teach genomics to undergraduates. The visual interface + makes complex concepts accessible, and students can perform real analysis without a + steep learning curve."</p> + </div> + <div class="testimonial-author"> + <div class="author-info"> + <h4>Dr. Sarah Chen</h4> + <p>Associate Professor, Molecular Biology</p> + </div> + </div> + </div> + + <div class="testimonial-card" data-aos="fade-up" data-aos-delay="100"> + <div class="testimonial-content"> + <p>"As a researcher focusing on genetic disorders, I appreciate DNAnalyzer's privacy-first + approach. The local server option allows me to analyze sensitive patient data without + exposing it to third parties."</p> + </div> + <div class="testimonial-author"> + <div class="author-info"> + <h4>Dr. Michael Rodriguez</h4> + <p>Genetic Researcher</p> + </div> + </div> + </div> + + <div class="testimonial-card" data-aos="fade-up" data-aos-delay="200"> + <div class="testimonial-content"> + <p>"The ability to quickly identify promoter regions and protein-coding sequences has + accelerated my synthetic biology project significantly. DNAnalyzer is now a core part of + our design verification process."</p> + </div> + <div class="testimonial-author"> + <div class="author-info"> + <h4>Emily Takahashi</h4> + <p>Synthetic Biology Engineer</p> + </div> + </div> + </div> + </div> + </div> + </section> + + <section class="section cta-section"> + <div class="container text-center"> + <h2>Ready to start analyzing DNA sequences?</h2> + <p>Experience the power of DNAnalyzer's features today</p> + + <div class="cta-buttons"> + <a href="../analyzer/analyzer.html" class="btn btn-primary"> + <i class="fas fa-dna btn-icon"></i> Try DNAnalyzer Now + </a> + <a href="../docs/docs.html" class="btn btn-secondary"> + <i class="fas fa-book btn-icon"></i> Read Documentation + </a> + </div> + </div> + </section> + </main> + + <!-- 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="footer-social"> + <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://www.twitter.com/DNAnalyzer_" class="social-link"> + <i class="fab fa-twitter"></i> + </a> + </div> + </div> + + <div class="footer-nav"> + <h4>Product</h4> + <ul> + <li><a href="features.html">Features</a></li> + <li><a href="../analyzer/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 © 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="features.js"></script> +</body> + +</html> \ No newline at end of file