{"id":13590,"date":"2024-07-18T14:05:42","date_gmt":"2024-07-18T18:05:42","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13590"},"modified":"2024-09-11T11:32:38","modified_gmt":"2024-09-11T15:32:38","slug":"new-blast-core-nucleotide-database","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/","title":{"rendered":"Get Faster, More Focused Search Results with NCBI\u2019s New BLAST Core Nucleotide Database (core_nt)"},"content":{"rendered":"<h3 aria-level=\"1\"><i><span data-contrast=\"auto\">Effective August 2024, core_nt will become the default<\/span><\/i><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h3>\n<p><span data-contrast=\"none\">Interested in faster nucleotide <\/span><a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-core-nt-20240717\"><span data-contrast=\"none\">BLAST<\/span><\/a><span data-contrast=\"none\"> searches with more focused search results? As <\/span><a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/11\/17\/re-evaluating-blast-nucleotide-nt\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-core-nt-20240717\"><span data-contrast=\"none\">previously announced<\/span><\/a><span data-contrast=\"none\">, NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it more compact and more efficient. Thanks to your feedback, NCBI\u2019s BLAST is excited to introduce the core nucleotide database (core_nt), an alternative to the default nt database that contains better-defined content and is less than half the size.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5 aria-level=\"2\">Benefits of BLAST core_nt over nt<\/h5>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"4\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:1080,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Enables faster searches \u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"4\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:1080,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"2\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Returns similar top results for most searches\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"4\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:1080,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"3\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Reduces redundancy for some highly represented organisms\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"4\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:1080,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"4\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Allows easier download and requires less storage space for database download for standalone BLAST\u00a0<\/span><\/li>\n<\/ul>\n<p><!--more--><\/p>\n<h5>What is core_nt?<\/h5>\n<p><span data-contrast=\"auto\">Core_nt contains the same eukaryotic transcript and gene-related sequences as nt. The core_nt database is nt without most eukaryotic chromosome sequences. Most nucleotide BLAST searches with core_nt will be similar to the nt database. However, core_nt is better than nt for accomplishing your most common BLAST search goals, such as identifying gene-related sequences like transcript sequences and complete bacterial chromosomes. This is because, in recent years, nt has acquired more low-relevance, non-annotated, and non-gene content.\u00a0<\/span><\/p>\n<p><b><span data-contrast=\"none\">Example:<\/span><\/b><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">The screenshots below show nucleotide BLAST results using the <\/span><i><span data-contrast=\"none\">Drosophila melanogaster<\/span><\/i><span data-contrast=\"none\"> rosy gene transcript (<\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NM_079613?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-core-nt-20240717\"><span data-contrast=\"none\">NM_079613<\/span><\/a><span data-contrast=\"none\">) as the search query. The <\/span><a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?CMD=Get&amp;RID=90TVZFE6016&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-core-nt-20240717\"><span data-contrast=\"none\">core_nt<\/span><\/a><span data-contrast=\"none\"> results (top panel) and the <\/span><a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?CMD=Get&amp;RID=712RGWJY013&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-core-nt-20240717\"><span data-contrast=\"none\">nt results<\/span><\/a><span data-contrast=\"none\"> (bottom panel) are the same for the top 12 results, which are mostly related transcript sequences from other <\/span><i><span data-contrast=\"none\">Drosophila<\/span><\/i><span data-contrast=\"none\"> species. With the original nt database, the majority of the remaining 100 results are dominated by unannotated <\/span><i><span data-contrast=\"none\">D. melanogaster<\/span><\/i><span data-contrast=\"none\"> chromosome assemblies (boxed in red) that provide no gene-related information.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">\u00a0<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\"> <img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"13592\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/core_nt_rosy\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?fit=884%2C1355&amp;ssl=1\" data-orig-size=\"884,1355\" 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=\"Core_nt_rosy\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?fit=196%2C300&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?fit=668%2C1024&amp;ssl=1\" class=\"alignright size-full wp-image-13592\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?resize=884%2C1355&#038;ssl=1\" alt=\"Screenshot of BLAST search results comparing core_nt (future default) and nt (current default).\" width=\"884\" height=\"1355\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?w=884&amp;ssl=1 884w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?resize=196%2C300&amp;ssl=1 196w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?resize=668%2C1024&amp;ssl=1 668w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?resize=98%2C150&amp;ssl=1 98w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?resize=768%2C1177&amp;ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/Core_nt_rosy.png?resize=176%2C270&amp;ssl=1 176w\" sizes=\"auto, (max-width: 884px) 100vw, 884px\" \/><\/span><\/p>\n<p>If you\u2019re interested in searching against eukaryote genome assemblies including full-length chromosomes, we suggest searching against the RefSeq Reference Genomes database (available in the BLAST database list) or individual assemblies from NCBI Datasets. Sets of genomes can also be searched through the WGS or microbial BLAST database options.<\/p>\n<h5><span style=\"font-size: 19px;\" data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">Try it out!\u00a0<\/span><\/h5>\n<p>Search our new <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;DATABASE=core_nt&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-core-nt-20240717\"><span data-contrast=\"none\">BLAST core_nt database<\/span><\/a><span data-contrast=\"none\"> and let us know what you think. S<\/span><span data-contrast=\"none\">hare your feedback using the yellow Feedback button located on the bottom of the BLAST webpage.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><b><span data-contrast=\"auto\">Please note:<\/span><\/b><span data-contrast=\"auto\"> As of August 2024, the new BLAST core_nt database will be the default. The original nt database will still be available as a choice in the database list.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5>Stay up to date<\/h5>\n<p><span data-contrast=\"none\">BLAST is a part of the\u202f<\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/comparative-genomics-resource\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-core-nt-20240717\"><span data-contrast=\"none\">NIH Comparative Genomics Resource (CGR)<\/span><\/a><span data-contrast=\"none\">. CGR facilitates reliable comparative genomics analyses\u202ffor all eukaryotic organisms through an NCBI Toolkit and community collaboration.\u202fFollow 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_50%22\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"none\">\u202fto keep up to date with BLAST and other CGR news.\u202f\u202f<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5>Questions?<\/h5>\n<p><span data-contrast=\"none\">If you have questions or would like to provide feedback, please reach out to us at <\/span><a href=\"mailto:info@ncbi.nlm.nih.gov\">info@ncbi.nlm.nih.gov<\/a>.<span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Effective August 2024, core_nt will become the default\u00a0 Interested in faster nucleotide BLAST searches with more focused search results? As previously announced, NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it more compact and more efficient. Thanks to your feedback, NCBI\u2019s BLAST is excited to introduce the core nucleotide database (core_nt), an &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Get Faster, More Focused Search Results with NCBI\u2019s New BLAST Core Nucleotide Database (core_nt)<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":13596,"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":"Get Faster, More Focused Search Results with NCBI\u2019s New BLAST Core Nucleotide Database (core_nt)","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":[77187,693060768,53114734],"table_tags":[],"class_list":["post-13590","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-blast","tag-comparative-genomics-resource-cgr","tag-blastn"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Get Faster, More Focused Search Results with NCBI\u2019s New BLAST Core Nucleotide Database (core_nt) - 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\/07\/18\/new-blast-core-nucleotide-database\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Get Faster, More Focused Search Results with NCBI\u2019s New BLAST Core Nucleotide Database (core_nt) - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Effective August 2024, core_nt will become the default\u00a0 Interested in faster nucleotide BLAST searches with more focused search results? As previously announced, NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it more compact and more efficient. Thanks to your feedback, NCBI\u2019s BLAST is excited to introduce the core nucleotide database (core_nt), an &hellip; Continue reading Get Faster, More Focused Search Results with NCBI\u2019s New BLAST Core Nucleotide Database (core_nt) &rarr;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/\" \/>\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=\"2024-07-18T18:05:42+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-09-11T15:32:38+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/BLAST_core_nt-3-e1721149899361.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=\"3 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\/07\/18\/new-blast-core-nucleotide-database\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Get Faster, More Focused Search Results with NCBI\u2019s New BLAST Core Nucleotide Database (core_nt)\",\"datePublished\":\"2024-07-18T18:05:42+00:00\",\"dateModified\":\"2024-09-11T15:32:38+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/\"},\"wordCount\":475,\"commentCount\":13,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/07\/BLAST_core_nt-3-e1721149899361.png?fit=1100%2C575&ssl=1\",\"keywords\":[\"Basic Local Alignment Search Tool (BLAST)\",\"Comparative Genomics Resource (CGR)\",\"Nucleotide BLAST (blastn)\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/07\/18\/new-blast-core-nucleotide-database\/\",\"name\":\"Get Faster, More Focused Search Results with NCBI\u2019s New BLAST Core Nucleotide Database (core_nt) - 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