{"id":10039,"date":"2022-11-17T10:37:01","date_gmt":"2022-11-17T15:37:01","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=10039"},"modified":"2023-05-04T14:06:25","modified_gmt":"2023-05-04T18:06:25","slug":"re-evaluating-blast-nucleotide-nt","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/11\/17\/re-evaluating-blast-nucleotide-nt\/","title":{"rendered":"Re-evaluating the BLAST Nucleotide Database (nt)"},"content":{"rendered":"<p>The ongoing sequencing revolution has resulted in exponential growth of the NCBI <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-nt-reevaluate-20221117\" target=\"_blank\" rel=\"noopener\">BLAST<\/a> databases. The default BLAST nucleotide database (nt), the most popular Web BLAST database, is currently 903 billion letters and continues to grow rapidly \u2013 doubling in size in the last year. This growth will cause longer search times, reduced capacity, and more delays in updating the database. In the not-too-distant future, searching the entire nt database on the web will no longer be possible unless we modify the database scope and composition.<\/p>\n<p>Because of the above concerns, we want to make the default Web BLAST nucleotide database smaller and more efficient. Some options are to:<\/p>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li>Change its composition to improve the quality of sequence entries included<\/li>\n<li>Take steps to slow its growth rate<\/li>\n<li>Divide it into several databases by biological or functional categories<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><!--more--><\/p>\n<p>Re-factoring of the database may be based on one of these strategies and will make use of feedback concerning your BLAST usage.<\/p>\n<p>To begin getting feedback, we have created a\u00a0page with four new databases based on taxonomic categories (Figure 1).<\/p>\n<p style=\"text-align: center;\"><a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-nt-reevaluate-20221117\"><strong>Please try the test databases and let us know what you think!<\/strong><\/a><\/p>\n<p><!--more--><\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"10042\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/11\/17\/re-evaluating-blast-nucleotide-nt\/sra\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?fit=1847%2C811&amp;ssl=1\" data-orig-size=\"1847,811\" 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=\"SRA\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?fit=300%2C132&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?fit=1024%2C450&amp;ssl=1\" class=\"alignnone size-full wp-image-10042\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?resize=1108%2C487&#038;ssl=1\" alt=\"\" width=\"1108\" height=\"487\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?w=1847&amp;ssl=1 1847w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?resize=300%2C132&amp;ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?resize=1024%2C450&amp;ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?resize=150%2C66&amp;ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?resize=768%2C337&amp;ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?resize=1536%2C674&amp;ssl=1 1536w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?resize=1200%2C527&amp;ssl=1 1200w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/11\/SRA.png?resize=270%2C119&amp;ssl=1 270w\" sizes=\"auto, (max-width: 1108px) 100vw, 1108px\" \/><\/p>\n<p><em>Figure 1. Database selection list on the <\/em><a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-nt-reevaluate-20221117\"><em>new test page<\/em><\/a><em>. This page has a possible database option that divides nt into four smaller databases by taxonomic\/functional categories. Inset: The Feedback button where you can provide your feedback about these databases and how you use BLAST.<\/em><\/p>\n<p>Please try searching with the test databases and tell us about your experience. How do you use the default nucleotide database? Do you mainly need quick matches to highly annotated records, or are you trying to find distantly related homologs to coding regions?<\/p>\n<p>Use the Feedback button on the results page and send us your thoughts and comments about BLAST databases.<\/p>\n<p>BLAST supports the\u00a0<a class=\"c-link\" tabindex=\"-1\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/comparative-genomics-resource\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-nt-reevaluate-20221117\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"https:\/\/www.ncbi.nlm.nih.gov\/comparative-genomics-resource\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=refseq-annotation-update-20221031\" data-sk=\"tooltip_parent\" data-remove-tab-index=\"true\">NIH Comparative Genomics Resource (CGR)<\/a>, an <a href=\"https:\/\/www.nlm.nih.gov\">NLM<\/a> project to establish an ecosystem to facilitate reliable comparative genomics analyses\u202ffor all eukaryotic organisms.<\/p>\n<p><a class=\"external-link\" href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_50%22\" rel=\"nofollow\">Join our mailing list<\/a> to keep up to date with BLAST and other CGR news.<\/p>\n<p><strong>Questions?<\/strong><\/p>\n<p>If you have questions, please reach out to us at <a href=\"mailto:blast-help@ncbi.nlm.nih.gov\">blast-help@ncbi.nlm.nih.gov<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The ongoing sequencing revolution has resulted in exponential growth of the NCBI BLAST databases. The default BLAST nucleotide database (nt), the most popular Web BLAST database, is currently 903 billion letters and continues to grow rapidly \u2013 doubling in size in the last year. This growth will cause longer search times, reduced capacity, and more &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/11\/17\/re-evaluating-blast-nucleotide-nt\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Re-evaluating the BLAST Nucleotide Database (nt)<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":10043,"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":"Re-evaluating the BLAST Nucleotide Database (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":[693060768,53114734],"table_tags":[],"class_list":["post-10039","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","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>Re-evaluating the BLAST Nucleotide Database (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\/2022\/11\/17\/re-evaluating-blast-nucleotide-nt\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Re-evaluating the BLAST Nucleotide Database (nt) - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"The ongoing sequencing revolution has resulted in exponential growth of the NCBI BLAST databases. The default BLAST nucleotide database (nt), the most popular Web BLAST database, is currently 903 billion letters and continues to grow rapidly \u2013 doubling in size in the last year. 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