86 lines
53 KiB
HTML
86 lines
53 KiB
HTML
<!DOCTYPE html>
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<html amp lang="en-US" data-amp-auto-lightbox-disable transformed="self;v=1" i-amphtml-layout="" i-amphtml-no-boilerplate="">
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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="Quick & Easy Access to Mpox Data Through NCBI Virus - NCBI Insights"><meta property="og:description" content="The World Health Organization (WHO) declared the recent upsurge of the mpox virus to be a public health emergency of international concern. Having timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. Therefore, NCBI’s GenBank is expediting the release of mpox data … Continue reading Quick & Easy Access to Mpox Data Through NCBI Virus →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2024/08/21/access-mpox-data-through-ncbi-virus/"><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="2024-08-21T15:38:57+00:00"><meta property="article:modified_time" content="2024-08-23T14:28:50+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/08/mpox_blog-1-e1724249484776.png"><meta property="og:image:width" content="1100"><meta property="og:image:height" content="575"><meta property="og:image:type" content="image/png"><meta name="author" content="NCBI Staff"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@NCBI"><meta name="twitter:site" content="@NCBI"><meta name="twitter:label1" content="Written by"><meta name="twitter:data1" content="NCBI Staff"><meta name="twitter:label2" content="Est. reading time"><meta name="twitter:data2" content="2 minutes"><meta name="robots" content="index, follow, max-image-preview:large, max-snippet:-1, max-video-preview:-1"><meta name="generator" content="AMP Plugin v2.5.5; mode=reader; theme=legacy"><script async="" src="https://cdn.ampproject.org/v0.mjs" type="module" crossorigin="anonymous"></script><script async nomodule src="https://cdn.ampproject.org/v0.js" crossorigin="anonymous"></script><script src="https://cdn.ampproject.org/v0/amp-social-share-0.1.mjs" async="" custom-element="amp-social-share" type="module" crossorigin="anonymous"></script><script async nomodule src="https://cdn.ampproject.org/v0/amp-social-share-0.1.js" crossorigin="anonymous" custom-element="amp-social-share"></script><style 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<h1 class="amp-wp-title">Quick & Easy Access to Mpox Data Through NCBI Virus</h1>
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<time datetime="2024-08-21T15:38:57+00:00">
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7 months ago </time>
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<amp-img width="1024" height="535" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/08/mpox_blog-1-e1724249484776.png?fit=1024%2C535&ssl=1" class="attachment-large size-large wp-post-image amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" alt="Virus cells in the background. Text says: NCBI Virus quick & easy access to Mpox data" data-hero-candidate="" layout="intrinsic" data-hero i-amphtml-ssr 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,PHN2ZyBoZWlnaHQ9IjUzNSIgd2lkdGg9IjEwMjQiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><img class="i-amphtml-fill-content i-amphtml-replaced-content" decoding="async" loading="lazy" alt="Virus cells in the background. Text says: NCBI Virus quick & easy access to Mpox data" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/08/mpox_blog-1-e1724249484776.png?fit=1024%2C535&ssl=1"></amp-img> </figure>
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<p><span data-contrast="none">The </span><a href="https://www.who.int/news/item/14-08-2024-who-director-general-declares-mpox-outbreak-a-public-health-emergency-of-international-concern"><span data-contrast="none">World Health Organization (WHO)</span></a> <span data-contrast="none">declared the</span><span data-contrast="none"> recent </span><span data-contrast="none">upsurge of the mpox virus to be a public health emergency of international concern. Having timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. </span><span data-contrast="none">Therefore, NCBI’s <a href="https://www.ncbi.nlm.nih.gov/genbank/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821">GenBank</a> is expediting the release of mpox data by annotating gene and coding region features as part of the submission process</span><span data-contrast="none">.</span><span data-ccp-props="{}"> </span></p>
|
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<p><span data-contrast="none">You can access mpox sequences </span><span data-contrast="none">shortly after public release</span><span data-contrast="none"> through </span><a href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821#/"><span data-contrast="none">NCBI Virus</span></a><span data-contrast="none">. </span><span data-contrast="none">Apply several filters to narrow down sequence records by collection date, release date, or the geographic region of origin and more. You can then quickly download FASTA sequences with customizable description lines or download the metadata table which includes accessions, submitter names, affiliated institutions, and the country of the institutions useful for citing the data sources.</span><span data-contrast="none"> </span><span data-ccp-props="{}"> </span></p>
|
||
<p>Use NCBI Datasets command-line (CLI) tool for programmatic access to mpox data. <a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821">Download and install</a> client. See our <a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/virus/virus-download/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821">how-to guide</a> to get started.</p>
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||
<h5><b><span data-contrast="none">Submit your data</span></b><span data-ccp-props="{}"> </span></h5>
|
||
<p><span data-contrast="none">Have you sequenced mpox virus isolates? Consider submitting your data to NCBI. Please submit raw sequence reads to </span><a href="https://submit.ncbi.nlm.nih.gov/about/sra/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821"><span data-contrast="none">Sequence Read Archive (SRA)</span></a><span data-contrast="none"> and assembled mpox sequences to </span><a href="https://www.ncbi.nlm.nih.gov/WebSub/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821"><span data-contrast="none">GenBank</span></a><span data-contrast="none">. Check out our </span><a href="https://www.ncbi.nlm.nih.gov/genbank/monkeypox_submission/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-mpox-20240821"><span data-contrast="none">step-by step instructions</span></a><span data-contrast="none"> to get started. Gene/protein annotation is not necessary for </span><span data-contrast="none">mpox sequence</span><span data-contrast="none"> submission</span><span data-contrast="none"> since it will be added by the GenBank team using </span><a href="https://github.com/ncbi/vadr"><span data-contrast="none">VADR</span></a>,<span data-contrast="none"> which was updated for mpox.</span><span data-ccp-props="{}"> </span></p>
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<h5><b><span data-contrast="none">Stay up to date</span></b><span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}'> </span></h5>
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<p><span data-contrast="none">Follow us on social </span><a href="https://twitter.com/ncbi"><span data-contrast="none">@NCBI</span></a><span data-contrast="none"> and </span><a href="https://public.govdelivery.com/accounts/USNLMOCPL/subscriber/new?topic_id=USNLMOCPL_52"><span data-contrast="none">join our mailing list</span></a><span data-contrast="none"> to keep up to date with GenBank and other NCBI news.</span><span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}'> </span></p>
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