{"id":9757,"date":"2022-10-11T14:16:17","date_gmt":"2022-10-11T18:16:17","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=9757"},"modified":"2022-10-11T14:17:07","modified_gmt":"2022-10-11T18:17:07","slug":"updated-prokaryote-representative-genomes-collection","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/","title":{"rendered":"Now available: Updated prokaryote representative genomes collection"},"content":{"rendered":"<p>An updated\u00a0<a class=\"external-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/assembly\/?term=%28Bacteria%5Borgn%5D+OR+Archaea%5Borgn%5D%29+AND+%28reference_genome%5Bfilter%5D+OR+representative_genome%5Bfilter%5D%29&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20221011\" target=\"_blank\" rel=\"nofollow noopener\">bacterial and archaeal representative genomes collection<\/a> is available! We selected a total of 16,665 of the 262,000 prokaryotic assemblies in RefSeq to <a class=\"external-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/about\/prokaryotes\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20221011\" target=\"_blank\" rel=\"nofollow noopener\">represent their respective species<\/a>. For the first time, more complete assemblies (as calculated by <a class=\"external-link\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25977477\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20221011\" target=\"_blank\" rel=\"nofollow noopener\">CheckM<\/a>) were ranked higher than less complete assemblies. See the ranked list of criteria for selecting representative assemblies <a class=\"external-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/about\/prokaryotes\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20221011#representative_genomes\" target=\"_blank\" rel=\"nofollow noopener\">here<\/a>. <!--more--><\/p>\n<p>The prokaryote genomes collection has grown by 4% since May 2022. A total of 610 species are represented for the first time. In addition, 204 species are represented by a better assembly (including 120 which are more complete), and 36 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.<\/p>\n<p>We updated the database on the\u00a0<a class=\"external-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch&amp;BLAST_SPEC=MicrobialGenomes&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20221011\" target=\"_blank\" rel=\"nofollow noopener\">Microbial Nucleotide BLAST page<\/a>\u00a0as well as the basic\u00a0<a class=\"external-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20221011\" target=\"_blank\" rel=\"nofollow noopener\">nucleotide BLAST RefSeq Representative genomes database<\/a>\u00a0(fourth in the menu) to reflect these changes. Finally, remember that you can now run\u00a0<a class=\"external-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastp&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20221011\" target=\"_blank\" rel=\"nofollow noopener\">BLAST searches against the proteins annotated on representative genomes<\/a> (second in the menu). Find more information <a class=\"external-link\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2020\/10\/16\/blast-refseq-select\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20221011\" target=\"_blank\" rel=\"nofollow noopener\">here<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>An updated\u00a0bacterial and archaeal representative genomes collection is available! We selected a total of 16,665 of the 262,000 prokaryotic assemblies in RefSeq to represent their respective species. For the first time, more complete assemblies (as calculated by CheckM) were ranked higher than less complete assemblies. See the ranked list of criteria for selecting representative assemblies &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Now available: Updated prokaryote representative genomes collection<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":8676,"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: Updated prokaryote representative genomes collection","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":[77187,34457,53114734,576953096,27739816],"table_tags":[],"class_list":["post-9757","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-blast","tag-taxonomy","tag-blastn","tag-prokaryotic-genome-annotation","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: Updated prokaryote representative genomes collection - 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\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Now available: Updated prokaryote representative genomes collection - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"An updated\u00a0bacterial and archaeal representative genomes collection is available! We selected a total of 16,665 of the 262,000 prokaryotic assemblies in RefSeq to represent their respective species. For the first time, more complete assemblies (as calculated by CheckM) were ranked higher than less complete assemblies. See the ranked list of criteria for selecting representative assemblies &hellip; Continue reading Now available: Updated prokaryote representative genomes collection &rarr;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/\" \/>\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=\"2022-10-11T18:16:17+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-10-11T18:17:07+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/06\/Prokaryotic-Representative-Genomes-Collection-Update-e1655849343472.png\" \/>\n\t<meta property=\"og:image:width\" content=\"697\" \/>\n\t<meta property=\"og:image:height\" content=\"375\" \/>\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=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Now available: Updated prokaryote representative genomes collection\",\"datePublished\":\"2022-10-11T18:16:17+00:00\",\"dateModified\":\"2022-10-11T18:17:07+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/\"},\"wordCount\":164,\"commentCount\":2,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/06\/Prokaryotic-Representative-Genomes-Collection-Update-e1655849343472.png?fit=697%2C375&ssl=1\",\"keywords\":[\"Basic Local Alignment Search Tool (BLAST)\",\"NCBI Taxonomy\",\"Nucleotide BLAST (blastn)\",\"Prokaryotic genome annotation\",\"RefSeq\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/11\/updated-prokaryote-representative-genomes-collection\/\",\"name\":\"Now available: Updated prokaryote representative genomes collection - 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