{"id":1237,"date":"2017-05-30T13:06:45","date_gmt":"2017-05-30T17:06:45","guid":{"rendered":"http:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=1237"},"modified":"2017-06-07T12:40:14","modified_gmt":"2017-06-07T16:40:14","slug":"virus-variation-resource-enhancements","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2017\/05\/30\/virus-variation-resource-enhancements\/","title":{"rendered":"NCBI\u2019s Virus Variation Resource Enhancements Include Standardized Search Criteria"},"content":{"rendered":"<p>NCBI\u2019s <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 \u2013 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>\n<p><!--more--><\/p>\n<figure id=\"attachment_1235\" aria-describedby=\"caption-attachment-1235\" style=\"width: 1194px\" class=\"wp-caption alignnone\"><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/viruses\/variation\/\" target=\"_blank\" rel=\"noopener noreferrer\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"1235\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/virus-variation-home_page\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2017\/05\/virus-variation-home_page.png?fit=1194%2C986&amp;ssl=1\" data-orig-size=\"1194,986\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"Virus Variation Home_page\" data-image-description=\"\" data-image-caption=\"&lt;p&gt;Figure 1. The Virus Variation Resource homepage. Modules for seven viral groups are at the top of the page.&lt;\/p&gt;\n\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2017\/05\/virus-variation-home_page.png?fit=300%2C248&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2017\/05\/virus-variation-home_page.png?fit=1024%2C846&amp;ssl=1\" class=\"wp-image-1235 size-full\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2017\/05\/virus-variation-home_page.png?resize=1108%2C915&#038;ssl=1\" alt=\"Virus Variation Homepage\" width=\"1108\" height=\"915\" \/><\/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>\n<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>\n<ul>\n<li>Search for sequences based on standardized gene and protein names as well as standardized sample information like host and isolation source.<\/li>\n<li>Generate standardized custom labels when downloading\u00a0and analyzing sequences in multiple sequence alignments and trees.<\/li>\n<li>Limit sequence searches to full-length proteins and\/or complete gene\/protein sets.<\/li>\n<li>Collapse identical sequences and use a single sequence to represent them in downloads and analyses.<\/li>\n<\/ul>\n<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, Sch\u00e4ffer AA, Brister JR. Virus Variation Resource &#8211; 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>\n<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>\n<figure id=\"attachment_1236\" aria-describedby=\"caption-attachment-1236\" style=\"width: 1372px\" class=\"wp-caption alignnone\"><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\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"1236\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/virus-variation-tree_viewer\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2017\/05\/virus-variation-tree_viewer.png?fit=1372%2C744&amp;ssl=1\" data-orig-size=\"1372,744\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"virus variation Tree_viewer\" data-image-description=\"\" data-image-caption=\"&lt;p&gt;Figure 2. The improved tree viewer.&lt;\/p&gt;\n\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2017\/05\/virus-variation-tree_viewer.png?fit=300%2C163&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2017\/05\/virus-variation-tree_viewer.png?fit=1024%2C555&amp;ssl=1\" class=\"alignnone size-full wp-image-1236\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2017\/05\/virus-variation-tree_viewer.png?resize=1108%2C601&#038;ssl=1\" alt=\"virus variation Tree viewer\" width=\"1108\" height=\"601\" \/><\/a><figcaption id=\"caption-attachment-1236\" class=\"wp-caption-text\"><strong>Figure 2.<\/strong> The improved tree viewer.<\/figcaption><\/figure>\n<p>To learn more about updated features and how to use them, please see\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/viruses\/variation\/help\/\" target=\"_blank\" rel=\"noopener noreferrer\">the Variation help page<\/a>.<\/p>\n<p>Please stay tuned as new annotation pipelines will soon be available for several viruses.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>NCBI\u2019s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses \u2013 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>\n","protected":false},"author":42204617,"featured_media":1235,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[386096,19751694,29189,861505,1012733,102671,2439,411420,15673026],"table_tags":[],"class_list":["post-1237","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-dengue","tag-ebolavirus","tag-influenza","tag-mers","tag-rotavirus","tag-variation","tag-viruses","tag-west-nile","tag-zika"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>NCBI\u2019s Virus Variation Resource Enhancements Include Standardized Search Criteria - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2017\/05\/30\/virus-variation-resource-enhancements\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"NCBI\u2019s Virus Variation Resource Enhancements Include Standardized Search Criteria - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"NCBI\u2019s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses \u2013 no more stumbling through multiple synonyms to find what you need. 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