90 lines
53 KiB
HTML
90 lines
53 KiB
HTML
<!DOCTYPE html>
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/*# sourceURL=/css/ampshared.css*/</style><meta property="og:locale" content="en_US"><meta property="og:type" content="article"><meta property="og:title" content="NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria - NCBI Insights"><meta property="og:description" content="NCBI’s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive pull-down menus. Virus Variation has modules for seven viral groups: influenza virus, Dengue virus, West … Continue reading NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/30/virus-variation-resource-enhancements/"><meta property="og:site_name" content="NCBI Insights"><meta property="article:publisher" content="https://www.facebook.com/ncbi.nlm"><meta property="article:published_time" content="2017-05-30T17:06:45+00:00"><meta property="article:modified_time" content="2017-06-07T16:40:14+00:00"><meta property="og:image" content="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2017/05/virus-variation-home_page.png?fit=1194%2C986&ssl=1"><meta property="og:image:width" content="1194"><meta property="og:image:height" content="986"><meta property="og:image:type" content="image/png"><meta name="author" content="NCBI Staff"><meta name="twitter:card" 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<h1 class="amp-wp-title">NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria</h1>
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<time datetime="2017-05-30T17:06:45+00:00">
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8 years ago </time>
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<p>NCBI’s <a href="http://www.ncbi.nlm.nih.gov/genome/viruses/variation/" target="_blank" rel="noopener noreferrer">Virus Variation</a> resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive pull-down menus.</p>
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<p></p>
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<figure id="attachment_1235" aria-describedby="caption-attachment-1235" class="wp-caption alignnone amp-wp-1319192" data-amp-original-style="width: 1194px"><a href="https://www.ncbi.nlm.nih.gov/genome/viruses/variation/" target="_blank" rel="noopener noreferrer"><amp-img class="wp-image-1235 size-full amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2017/05/virus-variation-home_page.png?resize=1108%2C915&ssl=1" alt="Virus Variation Homepage" width="1108" height="915" layout="intrinsic" i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjkxNSIgd2lkdGg9IjExMDgiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><noscript><img loading="lazy" decoding="async" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2017/05/virus-variation-home_page.png?resize=1108%2C915&ssl=1" alt="Virus Variation Homepage" width="1108" height="915"></noscript></amp-img></a><figcaption id="caption-attachment-1235" class="wp-caption-text"><strong>Figure 1.</strong> The Virus Variation Resource homepage. Modules for seven viral groups are at the top of the page.</figcaption></figure>
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<p>Virus Variation has modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A, and Zika virus. These modules now include a variety of new enhancements:</p>
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<ul>
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<li>Search for sequences based on standardized gene and protein names as well as standardized sample information like host and isolation source.</li>
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<li>Generate standardized custom labels when downloading and analyzing sequences in multiple sequence alignments and trees.</li>
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<li>Limit sequence searches to full-length proteins and/or complete gene/protein sets.</li>
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<li>Collapse identical sequences and use a single sequence to represent them in downloads and analyses.</li>
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</ul>
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<p>These updates were published in a recent paper in <em>Nucleic Acids Research</em>: Hatcher EL, Zhdanov SA, Bao Y, Blinkova O, Nawrocki EP, Ostapchuck Y, Schäffer AA, Brister JR. Virus Variation Resource – improved response to emergent viral outbreaks. Nucleic Acids Res. 2017 Jan 4;45(D1):D482-D490. doi: 10.1093/nar/gkw1065. Epub 2016 Nov 28. (<a href="https://www.ncbi.nlm.nih.gov/pubmed/27899678" target="_blank" rel="noopener noreferrer">https://www.ncbi.nlm.nih.gov/pubmed/27899678</a>).</p>
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<p>Finally, the Virus Variation resource also incorporates an improved tree viewer. Now you can locate individual isolates and highlight branches on phylogenetic or cluster trees using standardized metadata terms and other search criteria.</p>
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<figure id="attachment_1236" aria-describedby="caption-attachment-1236" class="wp-caption alignnone amp-wp-dd16557" data-amp-original-style="width: 1372px"><a href="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2017/05/virus-variation-tree_viewer.png?ssl=1" target="_blank" rel="noopener noreferrer"><amp-img class="alignnone size-full wp-image-1236 amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2017/05/virus-variation-tree_viewer.png?resize=1108%2C601&ssl=1" alt="virus variation Tree viewer" width="1108" height="601" layout="intrinsic" i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjYwMSIgd2lkdGg9IjExMDgiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><noscript><img loading="lazy" decoding="async" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2017/05/virus-variation-tree_viewer.png?resize=1108%2C601&ssl=1" alt="virus variation Tree viewer" width="1108" height="601"></noscript></amp-img></a><figcaption id="caption-attachment-1236" class="wp-caption-text"><strong>Figure 2.</strong> The improved tree viewer.</figcaption></figure>
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<p>To learn more about updated features and how to use them, please see <a href="https://www.ncbi.nlm.nih.gov/genome/viruses/variation/help/" target="_blank" rel="noopener noreferrer">the Variation help page</a>.</p>
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<p>Please stay tuned as new annotation pipelines will soon be available for several viruses.</p>
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