V-Score-Search/index.html at main · AnantharamanLab/V-Score-Search · GitHub

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<!DOCTYPE html>
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<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>V-Score Search</title>
    <link rel="stylesheet" href="./Software/styles.css">
    <script src="https://cdnjs.cloudflare.com/ajax/libs/PapaParse/5.3.0/papaparse.min.js"></script>
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<body>

    <!-- Header Image -->
    <img src="./Software/LabHeader.jpg" alt="Header of Lab" id="headerImage">

    <!-- Main Title -->
    <h1>V-Score Search</h1>

    <!-- Intro Section -->
    <div id="introSection">
        <p>
            <strong>V-Score-Search</strong> is a web-based platform designed for the public to explore
            V-scores and VL-scores across protein clusters from five major databases:
            PHROG, VOG, KEGG, Pfam, and eggNOG. These scores serve as quantitative
            "virus-like signatures" that differentiate viral from non-viral protein families and genomes.
            We demonstrate their utility through specific use cases, including virus identification,
            prophage discovery, and the annotation of host-derived or metabolic proteins within viral genomes.
            By defining the likelihood of a protein family’s viral origin, V-scores and VL-scores enable
            diverse applications in viral genomics, ecology, and evolution.
            For detailed methodology, please refer to our paper
            (<a href="https://www.biorxiv.org/content/10.1101/2024.10.24.619987v1" target="_blank">bioRxiv preprint</a>);
            to implement these metrics in your own viral identification, visit our
            <a href="https://github.com/AnantharamanLab/V-Score-Search" target="_blank">GitHub pipeline</a>.
        </p>
    </div>


    <div id="citationBlock">
        <strong>Citing V-Score-Search</strong>
        <p>
            If you find V-Score-Search useful, please consider citing the reference that describes this work:<br>
            Zhou K, Kosmopoulos JC, Colón ED, Badciong PJ, Anantharaman K.
            <em>V- and VL-Scores Unveil Viral Signatures and Origins of Protein Families.</em>
            (<a href="https://www.biorxiv.org/content/10.1101/2024.10.24.619987v1" target="_blank">
            https://www.biorxiv.org/content/10.1101/2024.10.24.619987v1
        </a>).
    </div>

    <!-- Keyword Search Title -->
    <h3 class="keyword-title">KEYWORD SEARCH</h3>

    <!-- Export + Search Link -->
    <div class="search-container" style="text-align:center; margin-bottom:15px;">
        <input type="text" id="searchInput" placeholder="Search...">
        <button id="goButton">Go</button>
        <button id="exampleButton">Example</button>
        <button id="exportButton">Export CSV</button>
    </div>

    <div id="searchInstructions">
        Enter any type of accession or ID to jump to the page for V-scores and VL-scores
        associated with every protein cluster or family. You can also search by protein name.
    </div>


    <!-- Data Table -->
    <table id="dataTable">
        <thead>
            <tr>
                <th class="sortable" data-column="Accession">Accession</th>
                <th class="sortable" data-column="Protein Function">Protein Function</th>
                <th class="sortable" data-column="V-Score">V-Score</th>
                <th class="sortable" data-column="V<sub>L</sub>-Score">V<sub>L</sub>-Score</th>
                <th class="sortable" data-column="Database">Database</th>
            </tr>
        </thead>
        <tbody>
            <!-- Data inserted dynamically -->
        </tbody>
    </table>

    <!-- Pagination -->
    <div id="pagination"></div>

    <!-- Footer with citations -->
    <footer>
        <p><strong>Citations:</strong></p>
        <ul>
            <li>Camargo AP, Roux S, Schulz F et al. Identification of mobile genetic elements with genomad. Nat Biotechnol. 2023;42:1303-12. <a href="https://doi.org/10.1038/s41587-023-01953-y" target="_blank">https://doi.org/10.1038/s41587-023-01953-y</a></li>
            <li>Hyatt D, Chen GL, Locascio PF et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 2010;11:1-11. <a href="https://doi.org/10.1186/1471-2105-11-119" target="_blank">https://doi.org/10.1186/1471-2105-11-119</a></li>
            <li>Mistry J, Chuguransky S, Williams L et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021;49:D412-D19. <a href="https://doi.org/10.1093/nar/gkaa913" target="_blank">https://doi.org/10.1093/nar/gkaa913</a></li>
            <li>Kanehisa M, Sato Y, Kawashima M et al. Kegg as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016;44:D457-D62.</li>
            <li>Eddy SR. Accelerated profile hmm searches. PLoS Comput Biol. 2011;7:e1002195.</li>
            <li>Larralde M, Zeller G. Pyhmmer: A python library binding to hmmer for efficient sequence analysis. Bioinformatics. 2023;39:btad214.</li>
            <li>Nayfach S, Camargo AP, Schulz F et al. Checkv assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol. 2020;39:578-85. <a href="https://doi.org/10.1038/s41587-020-00774-7" target="_blank">https://doi.org/10.1038/s41587-020-00774-7</a></li>
        </ul>
    </footer>

    <!-- Script -->
    <script src="./Software/script.js"></script>

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