{"id":5163,"date":"2021-01-12T17:31:18","date_gmt":"2021-01-12T22:31:18","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=5163"},"modified":"2021-01-12T17:51:26","modified_gmt":"2021-01-12T22:51:26","slug":"updated_prok-rep-assemblies","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/","title":{"rendered":"Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies!"},"content":{"rendered":"<p>We have updated the bacterial and archaeal <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/assembly\/?term=(Bacteria%5Borgn%5D%20OR%20Archaea%5Borgn%5D)%20AND%20(reference_genome%5Bfilter%5D%20OR%20representative_genome%5Bfilter%5D)&amp;utm_source=blog&amp;utm_medium=referrer&amp;utm_campaign=repr_genomes&amp;utm_term=release&amp;utm_content=20210112link1\">representative genome collection<\/a>!\u00a0 The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/about\/prokaryotes\/?utm_source=blog&amp;utm_medium=referrer&amp;utm_campaign=repr_genomes&amp;utm_term=release&amp;utm_content=20210112link2#representative_genomes\">represent<\/a> their respective species. The collection has increased by 11% since August 2020.\u00a0 We&#8217;ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and have removed 65 species because of changes in NCBI Taxonomy or uncertainty in their species assignment.<\/p>\n<p>We have also updated the\u00a0 Representative Genomes Database on the <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch&amp;BLAST_SPEC=MicrobialGenomes&amp;DATABASE=ref_prok_rep_genomes&amp;utm_source=blog&amp;utm_medium=referrer&amp;utm_campaign=repr_genomes&amp;utm_term=release&amp;utm_content=20210112link3\">Microbial Nucleotide BLAST page<\/a>\u00a0as well as the RefSeq Representative Genome Database on <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;DATABASE=refseq_representative_genomes&amp;utm_source=blog&amp;utm_medium=referrer&amp;utm_campaign=repr_genomes&amp;utm_term=release&amp;utm_content=20210112link4\">basic nucleotide BLAST<\/a>, to reflect these changes.<!--more--><\/p>\n<p>You can download the reference and representative set from the\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/assembly\/?term=(Bacteria%5Borgn%5D%20OR%20Archaea%5Borgn%5D)%20AND%20(reference_genome%5Bfilter%5D%20OR%20representative_genome%5Bfilter%5D)&amp;utm_source=blog&amp;utm_medium=referrer&amp;utm_campaign=repr_genomes&amp;utm_term=release&amp;utm_content=20210112link5\">Assembly<\/a> resource. If you are interested in the annotation on these genomes, you can limit searches to proteins annotated on representative genomes by adding &#8220;refseq_select<span class=\"error\">[filter]&#8221;<\/span>\u00a0to any query in the\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protein?utm_source=blog&amp;utm_medium=referrer&amp;utm_campaign=repr_genomes&amp;utm_term=release&amp;utm_content=20210112link6\">Protein<\/a>\u00a0database. For example, you can find all proteins annotated on representative genomes in the genus\u00a0<em>Klebsiella<\/em> by using the query: &#8220;<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protein\/?term=Klebsiella%5Borganism%5D%C2%A0AND%20refseq_select%5Bfilter%5D&amp;utm_source=blog&amp;utm_medium=referrer&amp;utm_campaign=repr_genomes&amp;utm_term=release&amp;utm_content=20210112link7\">Klebsiella<span class=\"error\">[organism]<\/span>\u00a0AND refseq_select<span class=\"error\">[filter]&#8221;<\/span><\/a>.<\/p>\n<p>And you can now run Blast searches against proteins annotated on representative genomes. Go to the <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastp&amp;PAGE_TYPE=BlastSearch&amp;DATABASE=refseq_select_prot&amp;EQ_MENU=bacteria%20%20%28taxid%3A2%29&amp;EQ_MENU1=archaea%20%20(taxid:2157)&amp;NUM_ORG=2&amp;utm_source=blog&amp;utm_medium=referrer&amp;utm_campaign=repr_genomes&amp;utm_term=release&amp;utm_content=20210112link8\">protein-protein BLAST page<\/a> and choose the &#8216;RefSeq Select (refseq_select)&#8217; database . See\u00a0 our recent <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2020\/10\/16\/blast-refseq-select\/\">post<\/a> for more information.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>We have updated the bacterial and archaeal representative genome collection!\u00a0 The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 11% since August 2020.\u00a0 We&#8217;ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies!<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":0,"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":"Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies!","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":[6595,3064946,576953096,9715,693060689],"table_tags":[],"class_list":["post-5163","post","type-post","status-publish","format-standard","hentry","category-whats-new","tag-assembly","tag-nucleotide","tag-prokaryotic-genome-annotation","tag-protein","tag-representative-genome"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies! - 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\/2021\/01\/12\/updated_prok-rep-assemblies\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies! - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"We have updated the bacterial and archaeal representative genome collection!\u00a0 The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 11% since August 2020.\u00a0 We&#8217;ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and &hellip; Continue reading Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies! &rarr;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/\" \/>\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=\"2021-01-12T22:31:18+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2021-01-12T22:51:26+00:00\" \/>\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\/2021\/01\/12\/updated_prok-rep-assemblies\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies!\",\"datePublished\":\"2021-01-12T22:31:18+00:00\",\"dateModified\":\"2021-01-12T22:51:26+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/\"},\"wordCount\":206,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"keywords\":[\"Assembly\",\"NCBI Nucleotide\",\"Prokaryotic genome annotation\",\"Protein\",\"Representative genome\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/\",\"name\":\"Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies! 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The collection has increased by 11% since August 2020.\u00a0 We&#8217;ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and &hellip; Continue reading Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies! &rarr;","og_url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/","og_site_name":"NCBI Insights","article_publisher":"https:\/\/www.facebook.com\/ncbi.nlm","article_published_time":"2021-01-12T22:31:18+00:00","article_modified_time":"2021-01-12T22:51:26+00:00","author":"NCBI Staff","twitter_card":"summary_large_image","twitter_creator":"@NCBI","twitter_site":"@NCBI","twitter_misc":{"Written by":"NCBI Staff","Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/#article","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/"},"author":{"name":"NCBI Staff","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b"},"headline":"Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies!","datePublished":"2021-01-12T22:31:18+00:00","dateModified":"2021-01-12T22:51:26+00:00","mainEntityOfPage":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/"},"wordCount":206,"commentCount":0,"publisher":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization"},"keywords":["Assembly","NCBI Nucleotide","Prokaryotic genome annotation","Protein","Representative genome"],"articleSection":["What's New"],"inLanguage":"en-US","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/","url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/01\/12\/updated_prok-rep-assemblies\/","name":"Prokaryotic representative genomes updated \u2014 now over 13 thousand assemblies! 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