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{"id":13229,"date":"2024-05-07T11:55:38","date_gmt":"2024-05-07T15:55:38","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13229"},"modified":"2024-05-07T13:52:26","modified_gmt":"2024-05-07T17:52:26","slug":"may-2024-pgap","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/05\/07\/may-2024-pgap\/","title":{"rendered":"New! May 2024 Release of Stand-Alone PGAP"},"content":{"rendered":"<div id=\"descriptionmodule\" class=\"module toggle-wrap \">\n<div class=\"mod-content\">\n<div id=\"description-val\" class=\"field-ignore-highlight editable-field inactive\" title=\"Click to edit\">\n<div class=\"user-content-block\">\n<p>We are happy to announce the release of a <a href=\"https:\/\/github.com\/ncbi\/pgap\/releases\/tag\/2024-04-27.build7426\">new version<\/a> of the stand-alone <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/annotation_prok\/release_notes\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pgap-release-20240507\">Prokaryotic Genome Annotation Pipeline<\/a> (PGAP).<\/p>\n<h5>What’s new? <!--more--><\/h5>\n<ul>\n<li><span style=\"font-size: 17px;\">Updated software<\/span>\n<ul>\n<li><span style=\"font-size: 17px;\">hmmer v.3.4<\/span><\/li>\n<li><span style=\"font-size: 17px;\">infernal 1.1.5\u00a0<\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"font-size: 17px;\">Updated support\u00a0<\/span>\n<ul>\n<li><span style=\"font-size: 17px;\">Support for <a href=\"https:\/\/en.wikipedia.org\/wiki\/Apple_silicon\">Apple Silicon<\/a> using <a href=\"https:\/\/www.docker.com\/blog\/docker-desktop-4-26\/\">Docker Desktop<\/a> \/ Rosetta<\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"font-size: 17px;\">Revised ANI results<\/span>\n<ul>\n<li><span style=\"font-size: 17px;\">Revised report generation for Average Nucleotide Identity (ANI) Taxonomy checks, including significant overhaul of how ANI contamination is computed and reported. See the <a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/all\/README.txt\">README<\/a> on the FTP site for additional details.\u00a0<\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"font-size: 17px;\">Ongoing improved protein family model data used for annotation<\/span>\n<ul>\n<li><span style=\"font-size: 17px;\">PGAP assigns function to predicted proteins based on hits to <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protfam?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pgap-release-20240507\">Protein Family Models<\/a>, such as protein profile HMMs, BLAST hits, and domain architectures.\u00a0<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>As with every previous release, this release comes with incremental improvements by expert curators of the Protein Family Model collection that drives the precision of PGAP\u2019s structural and functional annotation.<\/p>\n<h5 aria-level=\"5\"><b><span data-contrast=\"auto\">Stay up to date<\/span><\/b><span data-ccp-props=\"{"134245418":true,"134245529":true,"201341983":0,"335557856":16777215,"335559738":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">Follow us on social media\u202f<\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"auto\">\u202fand\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"auto\">\u202fto keep up to date with\u202fPGAP\u202fand other NCBI news.<\/span><span data-ccp-props=\"{"134233117":false,"134233118":false,"201341983":0,"335557856":16777215,"335559738":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5 aria-level=\"2\"><b><span data-contrast=\"auto\">Questions?<\/span><\/b><span data-ccp-props=\"{"134245418":true,"134245529":true,"201341983":0,"335559738":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/h5>\n<p aria-level=\"2\"><span data-contrast=\"auto\">Please\u00a0<\/span><a href=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\"><span data-contrast=\"none\">reach out to us<\/span><\/a><span data-contrast=\"auto\">\u00a0with questions or feedback.<\/span><span data-ccp-props=\"{"134245418":true,"134245529":true,"201341983":0,"335559738":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"addcomment\" class=\"module sticky\" data-sticky-comment-enabled=\"true\">\n<div id=\"addcomment-inner\" class=\"module\">\n<div class=\"mod-footer\">\n<div class=\"addcomment-action\"><a id=\"footer-comment-button\" href=\"https:\/\/jira.ncbi.nlm.nih.gov\/secure\/AddComment!default.jspa?id=1955359\" name=\"add-comment\"><\/a><\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>We are happy to announce the release of a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP). What’s new?<\/p>\n","protected":false},"author":42204617,"featured_media":11620,"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! May 2024 Release of Stand-Alone PGAP","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":[693060700,15779425,693060702],"table_tags":[],"class_list":["post-13229","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-hidden-markov-models-hmm","tag-pgap","tag-protein-family-model"],"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! 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