{"id":13138,"date":"2024-04-22T10:21:13","date_gmt":"2024-04-22T14:21:13","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13138"},"modified":"2024-04-22T10:21:13","modified_gmt":"2024-04-22T14:21:13","slug":"cleaner-blast-databases-more-accurate-results","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/04\/22\/cleaner-blast-databases-more-accurate-results\/","title":{"rendered":"Cleaner BLAST Databases for More Accurate Results"},"content":{"rendered":"<h4><i><span data-contrast=\"auto\">Removing contaminated sequences using NCBI quality assurance tools<\/span><\/i><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/h4>\n<p><span data-contrast=\"auto\">Do you use <\/span><a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-cleaner-20240422\"><span data-contrast=\"none\">BLAST<\/span><\/a><span data-contrast=\"auto\"> to identify a sequence or the evolutionary scope of a gene? That can be challenging if contaminated and misclassified sequences are in the BLAST databases and show up in your search results. To address<\/span><span data-contrast=\"auto\"> this problem<\/span><span data-contrast=\"auto\">, we now use the NCBI quality assurance tools listed below to systematically remove these misleading sequences from the default nucleotide (nt) and protein (nr) BLAST databases.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><!--more--><\/p>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&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;\"><a href=\"https:\/\/github.com\/ncbi\/fcs\">Foreign Contamination Screen tool for genome cross-species screening (FCS-GX)<\/a> detects contamination from foreign organisms in genomes and other sequences using the genome cross-species aligner (GX)\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&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;\"><a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/05\/27\/ani-for-assembly-validation?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-cleaner-20240422\">Average Nucleotide Identity (ANI)<\/a> evaluates the taxonomic classification of prokaryotic genome assemblies. Sequences from genomes marked up as \u2018unverified source organism\u2019 are considered suspect and removed.\u00a0<\/span><\/li>\n<\/ul>\n<p><span data-contrast=\"auto\">This process has removed approximately 2.23% of sequences from nr and 0.01% from nt. Lists of nucleotide and protein sequences identified as contaminant or misclassified are available from our <a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/TOOLS\/FCS\/reports\/blast_contam_lists\/\">FTP site<\/a>.<\/span> <span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/p>\n<h5>Stay up to date<\/h5>\n<p><span data-contrast=\"none\">BLAST is 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-cleaner-20240422\"><span data-contrast=\"none\">NIH Comparative Genomics Resource (CGR)<\/span><\/a><span data-contrast=\"none\">.\u202fCGR facilitates reliable comparative genomics analyses\u202ffor all eukaryotic organisms through an NCBI Toolkit and community collaboration.\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<p><span data-contrast=\"none\">Follow us on social\u202f<\/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.<\/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\">We want to hear from you! Try it out and let us know what you think. We are making ongoing improvements based on your feedback. If you have questions or would like to provide feedback, please reach out to us 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\">.\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","protected":false},"excerpt":{"rendered":"<p>Removing contaminated sequences using NCBI quality assurance tools\u00a0 Do you use BLAST to identify a sequence or the evolutionary scope of a gene? That can be challenging if contaminated and misclassified sequences are in the BLAST databases and show up in your search results. To address this problem, we now use the NCBI quality assurance &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/04\/22\/cleaner-blast-databases-more-accurate-results\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Cleaner BLAST Databases for More Accurate Results<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":13158,"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":"Cleaner BLAST Databases for More Accurate Results","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":[77187,693060768,693060858],"table_tags":[],"class_list":["post-13138","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-blast","tag-comparative-genomics-resource-cgr","tag-foreign-contamination-screen-fcs-tool"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Cleaner BLAST Databases for More Accurate Results - 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\/04\/22\/cleaner-blast-databases-more-accurate-results\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Cleaner BLAST Databases for More Accurate Results - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Removing contaminated sequences using NCBI quality assurance tools\u00a0 Do you use BLAST to identify a sequence or the evolutionary scope of a gene? 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