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{"id":8357,"date":"2022-05-24T07:56:50","date_gmt":"2022-05-24T11:56:50","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=8357"},"modified":"2022-05-24T07:56:50","modified_gmt":"2022-05-24T11:56:50","slug":"new-in-rapt","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/05\/24\/new-in-rapt\/","title":{"rendered":"New in RAPT: Better taxonomic assignment and GO annotation"},"content":{"rendered":"<p>We are excited to announce two improvements to the Read assembly and Annotation Pipeline Tool (<a class=\"external-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/rapt?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=RAPT&utm_content=20220517link1\" target=\"_blank\" rel=\"nofollow noopener\">RAPT<\/a>), which allows you to assemble genomic reads for bacterial or archaeal isolates and annotate their genes at the click of a button.<\/p>\n<h4>Improved taxonomic assignment<\/h4>\n<p>Now RAPT verifies the scientific name you provide with the reads, and corrects it as needed with the Average Nucleotide Identity (<a class=\"external-link\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29792589\/?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=ANI&utm_content=20220524link2\" target=\"_blank\" rel=\"nofollow noopener\">ANI<\/a>) tool, which compares your genome to type strain assemblies in <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=GenBank&utm_content=20220524link3\">GenBank<\/a> to place it in the taxonomic tree. So, even if you only have a rough idea of the species you have sequenced, input datasets tailored to your genome will be used for the annotation and you will get the best possible gene set from RAPT. <!--more--><\/p>\n<h4>Gene Ontology<\/h4>\n<p>Genes are now assigned <a class=\"external-link\" href=\"http:\/\/geneontology.org\/\" target=\"_blank\" rel=\"nofollow noopener\">Gene Ontology<\/a>\u00a0(GO) terms when possible. The terms are derived from the collection of\u00a0<a class=\"external-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/protfam?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=protfam&utm_content=20220524link4\" target=\"_blank\" rel=\"nofollow noopener\">Protein Family Models<\/a> (hidden Markov models, BlastRules and conserved domain architectures) used by RAPT to name the proteins. On average, a third of Coding Sequences (CDSs) annotated by RAPT will get at least one GO term. We are actively working on mapping more GO terms to our Protein Family Models, so this percentage will grow with time. See more information in this\u00a0<a class=\"external-link\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/02\/24\/gene-ontology-refseq\/?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=GOterms-RefSeq&utm_content=20220517link5\" target=\"_blank\" rel=\"nofollow noopener\">blog post<\/a>.<\/p>\n<p>If you prefer to run RAPT on your own local machine or on the cloud, please visit our\u00a0<a class=\"external-link\" href=\"https:\/\/github.com\/ncbi\/rapt\/\" target=\"_blank\" rel=\"nofollow noopener\">github site<\/a>\u00a0to get started.<\/p>\n<p>==============<\/p>\n<h4>New to RAPT?<\/h4>\n<p>RAPT is an easy-to-use pilot service for the <em>de novo<\/em>\u00a0assembly and gene annotation of public or private Illumina genomic reads sequenced from bacterial or archaeal isolates. RAPT consists of three major components, the genome assembler\u00a0<a class=\"external-link\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/30286803\/?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=SKESA&utm_content=20220524link6\" target=\"_blank\" rel=\"nofollow noopener\">SKESA<\/a>, the taxonomic assignment tool\u00a0<a class=\"external-link\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/29792589\/?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=ANI&utm_content=20220524link7\" target=\"_blank\" rel=\"nofollow noopener\">ANI<\/a>\u00a0and the Prokaryotic Genome Annotation Pipeline (<a class=\"external-link\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27342282\/?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=PGAP&utm_content=20220524link8\" target=\"_blank\" rel=\"nofollow noopener\">PGAP<\/a>), and produces an annotated genome of quality comparable to <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=RefSeq&utm_content=20220524link9\">RefSeq<\/a> in a couple of hours.<\/p>\n<p>Find more information about RAPT <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/12\/assemble-annotate-prokaryotic-genomes-webrapt\/?utm_source=blog&utm_medium=referral&utm_campaign=RAPT-new-features&utm_term=assemble-annotate-RAPT&utm_content=20220524link10\">here<\/a> and check out our video!<\/p>\n<div class=\"jetpack-video-wrapper\"><iframe loading=\"lazy\" title=\"Introducing RAPT, a Web Service for the Read Assembly and Annotation Pipeline Tool\" width=\"1108\" height=\"623\" src=\"https:\/\/www.youtube.com\/embed\/GVPnETb64XA?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe><\/div>\n<p> <\/p>\n","protected":false},"excerpt":{"rendered":"<p>We are excited to announce two improvements to the Read assembly and Annotation Pipeline Tool (RAPT), which allows you to assemble genomic reads for bacterial or archaeal isolates and annotate their genes at the click of a button. Improved taxonomic assignment Now RAPT verifies the scientific name you provide with the reads, and corrects it … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/05\/24\/new-in-rapt\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">New in RAPT: Better taxonomic assignment and GO annotation<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":8428,"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":"New in RAPT: Better taxonomic assignment and GO annotation","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":[1201719,693060756,15779425,693060702,693060699,27739816,693060708],"table_tags":[],"class_list":["post-8357","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-genbank","tag-gene-ontology-go","tag-pgap","tag-protein-family-model","tag-rapt","tag-refseq","tag-skesa"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>New in RAPT: Better taxonomic assignment and GO annotation - 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\/05\/24\/new-in-rapt\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"New in RAPT: Better taxonomic assignment and GO annotation - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"We are excited to announce two improvements to the Read assembly and Annotation Pipeline Tool (RAPT), which allows you to assemble genomic reads for bacterial or archaeal isolates and annotate their genes at the click of a button. 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