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{"id":13676,"date":"2024-08-05T08:55:53","date_gmt":"2024-08-05T12:55:53","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13676"},"modified":"2024-08-05T08:55:53","modified_gmt":"2024-08-05T12:55:53","slug":"assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/","title":{"rendered":"Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus"},"content":{"rendered":"<p><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/virus?SeqType_s=Genome&VirusLineage_ss=Influenza%20A%20virus,%20taxid:11320\"><span data-contrast=\"none\">NCBI Virus<\/span><\/a> now offers genomes for viruses such as Influenza A by using an automated process to group segments from the same samples.<span data-contrast=\"auto\"> We group these segments into genomes based on metadata for the sample including <\/span><span data-contrast=\"none\">species, isolate name, host organism, collection date, and location. Newly released <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-improvements-20240805\"><span data-contrast=\"none\">GenBank<\/span><\/a><span data-contrast=\"none\"> records are added daily.<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">Access these genome assemblies through <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/virus?SeqType_s=Genome&VirusLineage_ss=Influenza%20A%20virus,%20taxid:11320\"><span data-contrast=\"none\">NCBI Virus<\/span><\/a><span data-contrast=\"none\"> using the new <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/virus?SeqType_s=Genome&VirusLineage_ss=Influenza%20A%20virus,%20taxid:11320\"><span data-contrast=\"none\">“<\/span><\/a><span data-contrast=\"none\">NCBI Virus Assembly” tab<\/span><span data-contrast=\"none\"> above the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/virus?SeqType_s=Genome&VirusLineage_ss=Influenza%20A%20virus,%20taxid:11320\"><span data-contrast=\"none\">Results Table<\/span><\/a><span data-contrast=\"none\"> as shown below. <\/span><!--more--><\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"13667\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?attachment_id=13667\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?fit=1195%2C813&ssl=1\" data-orig-size=\"1195,813\" data-comments-opened=\"1\" data-image-meta=\"{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}\" data-image-title=\"virus_results_browser_assembly_tab\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?fit=300%2C204&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?fit=1024%2C697&ssl=1\" class=\"alignright size-full wp-image-13667\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?resize=1108%2C754&ssl=1\" alt=\"Screen shot to show how to access genome assemblies through NCBI Virus using the new "NCBI Virus Assembly" tab above the Results Table.\" width=\"1108\" height=\"754\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?w=1195&ssl=1 1195w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?resize=300%2C204&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?resize=1024%2C697&ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?resize=150%2C102&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?resize=768%2C522&ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/virus_results_browser_assembly_tab.png?resize=270%2C184&ssl=1 270w\" sizes=\"auto, (max-width: 1108px) 100vw, 1108px\" \/><\/p>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Currently, genome groups are only being built for Influenza A, B, and C, and only if the expected number of segments is present\u00a0\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"2\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">We plan to expand this effort to include other segmented viruses and partial genomes. Please <a href=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\">contact us<\/a> if you would like genome groups for a particular virus species<\/span><\/li>\n<\/ul>\n<h5>What\u2019s new?<\/h5>\n<p><span data-contrast=\"none\">NCBI Virus has made several updates to the interface to support access to the genomes:<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/p>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"3\" data-list-defn-props=\"{"335552541":1,"335559685":768,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"3\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">The “RefSeq Genome” tab is deprecated, and the \u201cNCBI Virus Assembly\u201d tab now includes both GenBank assemblies of grouped segments and RefSeq assemblies\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"3\" data-list-defn-props=\"{"335552541":1,"335559685":768,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"4\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">New column for Assembly accessions in the \u201cNucleotide\u201d and \u201cProtein\u201d tabs\u00a0\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"3\" data-list-defn-props=\"{"335552541":1,"335559685":768,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"5\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">New Segment filter (works best after first selecting a virus group using the Virus\/Taxonomy filter)\u00a0<\/span><\/li>\n<\/ul>\n<p><span data-contrast=\"auto\">Filters have been improved by adding definitions and hints for how to best apply the filters. <\/span><span data-contrast=\"none\">Several filters have also been renamed, although their functionality and data scope remain the same:<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/p>\n<table data-tablestyle=\"MsoTableGrid\" data-tablelook=\"1696\" aria-rowcount=\"10\">\n<tbody>\n<tr aria-rowindex=\"1\">\n<td data-celllook=\"65536\"><span style=\"font-size: 16px;\"><b>Original Name<\/b>\u00a0<\/span><\/td>\n<td data-celllook=\"65536\"><span style=\"font-size: 16px;\"><b>New Name<\/b>\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"2\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Genome Completeness\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Assembly Completeness\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"3\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Virus\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Virus\/Taxonomy\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"4\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Sequence Type\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">GenBank\/RefSeq\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"5\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Random Sampling\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Surveillance Sampling\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"6\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Isolate\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Isolate\/Strain Name\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"7\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Proteins\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Has Protein\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"8\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Provirus\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Provirus\/Integrated\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"9\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Isolation Source\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Tissue\/Specimen\/Source\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"10\">\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Lab Host\u00a0<\/span><\/td>\n<td data-celllook=\"0\"><span style=\"font-size: 16px;\">Lab Passaged\u00a0<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5>Learn more<\/h5>\n<p><span data-contrast=\"none\">For more information, see <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/docs\/help\/?utm_source=ncbi_insights&utm_medium=referral&utm_term=virus-improvements-20240805#recent-changes\"><span data-contrast=\"none\">NCBI Virus help documentation<\/span><\/a><span data-contrast=\"none\">.\u00a0<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Stay up to date<\/h5>\n<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\">\u202fand\u202f<\/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\">\u202fto keep up to date with NCBI Virus and other NCBI news.<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Questions?<\/h5>\n<p><span data-contrast=\"none\">Feel free to contact our Help Desk at\u202f<\/span><a href=\"mailto:info@ncbi.nlm.nih.gov\"><span data-contrast=\"none\">info@ncbi.nlm.nih.gov<\/span><\/a><span data-contrast=\"none\">\u202fif you have any questions or concerns.<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335557856":16777215,"335559740":240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>NCBI Virus now offers genomes for viruses such as Influenza A by using an automated process to group segments from the same samples. We group these segments into genomes based on metadata for the sample including species, isolate name, host organism, collection date, and location. Newly released GenBank records are added daily.\u00a0 Access these genome … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":13668,"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":"Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[6595,1201719,693060764,27739816],"table_tags":[],"class_list":["post-13676","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-assembly","tag-genbank","tag-ncbi-virus","tag-refseq"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus - 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\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"NCBI Virus now offers genomes for viruses such as Influenza A by using an automated process to group segments from the same samples. We group these segments into genomes based on metadata for the sample including species, isolate name, host organism, collection date, and location. Newly released GenBank records are added daily.\u00a0 Access these genome … Continue reading Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus →\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/\" \/>\n<meta property=\"og:site_name\" content=\"NCBI Insights\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/ncbi.nlm\" \/>\n<meta property=\"article:published_time\" content=\"2024-08-05T12:55:53+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/NCBI_Virus_Blog-2-e1722527201197.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1100\" \/>\n\t<meta property=\"og:image:height\" content=\"575\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"NCBI Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@NCBI\" \/>\n<meta name=\"twitter:site\" content=\"@NCBI\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"NCBI Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus\",\"datePublished\":\"2024-08-05T12:55:53+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/\"},\"wordCount\":331,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/08\/NCBI_Virus_Blog-2-e1722527201197.png?fit=1100%2C575&ssl=1\",\"keywords\":[\"Assembly\",\"GenBank\",\"NCBI Virus\",\"RefSeq\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/08\/05\/assembled-genomes-influenza-viruses-improved-functionality-ncbi-virus\/\",\"name\":\"Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus - 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