{"id":15,"date":"2024-04-04T08:51:36","date_gmt":"2024-04-04T05:51:36","guid":{"rendered":"https:\/\/sisu.ut.ee\/eukaryome\/other-similar-databases\/"},"modified":"2024-10-22T12:55:31","modified_gmt":"2024-10-22T09:55:31","slug":"other-similar-databases","status":"publish","type":"page","link":"https:\/\/sisu.ut.ee\/eukaryome\/other-similar-databases\/","title":{"rendered":"Other databases and resources"},"content":{"rendered":"<h2 dir=\"ltr\" style=\"text-align: justify;\">Other databases<\/h2>\n<p dir=\"ltr\" style=\"text-align: justify;\">Maintaining reference databases requires accurate and high-quality sequence data, as well as meticulous annotation and regular updates to reflect the rapidly expanding knowledge of bio diversity. Taxonomic annotation of sequencing data is provided in the following databases:<\/p>\n<ul>\n<li><a href=\"https:\/\/unite.ut.ee\/\">UNITE database<\/a>\n<ul>\n<li style=\"text-align: justify;\">based on the ITS region covers all eukaryotes with the main focus on Fungi<\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/www.arb-silva.de\/\">SILVA database<\/a>\n<ul>\n<li style=\"text-align: justify;\">includes SSU and LSU genes, from both amplicons and (meta)genomes<\/li>\n<\/ul>\n<\/li>\n<li style=\"text-align: justify;\">\u00a0<a href=\"https:\/\/pr2-database.org\/\">PR2 database<\/a>\n<ul>\n<li style=\"text-align: justify;\">includes the SSU gene and mainly focuses on protists<\/li>\n<\/ul>\n<\/li>\n<li role=\"presentation\"><a title=\"\" href=\"https:\/\/github.com\/WormsEtAl\/18SNemaBase\" target=\"_blank\" rel=\"noopener\" data-url=\"https:\/\/github.com\/WormsEtAl\/18SNemaBase\">18S-Nemabase<\/a>\n<ul>\n<li role=\"presentation\">focuses on SSU gene of nematode<\/li>\n<\/ul>\n<\/li>\n<li role=\"presentation\"><a href=\"https:\/\/www.boldsystems.org\/\">BOLD<\/a>\n<ul>\n<li role=\"presentation\">focus on COI of animals<\/li>\n<\/ul>\n<\/li>\n<li role=\"presentation\"><a href=\"http:\/\/www.reference-midori.info\/\">MIDORI<\/a>\n<ul>\n<li role=\"presentation\">Eukaryota mitochondrial DNA sequences<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p dir=\"ltr\" style=\"text-align: justify;\">In comparison with the above databases, <strong>the EUKARYOME utilizes additionally long reads spanning the SSU, ITS, and LSU regions<\/strong>, which would be essential for chimera filtering and improved identification using ultra-long reads.<\/p>\n<h2 style=\"text-align: justify;\">Software:<\/h2>\n<ul>\n<li><a href=\"https:\/\/pipecraft2-manual.readthedocs.io\/en\/latest\/\">PipeCraft2<\/a> \u2013 metabarcoding data analyses platform with graphical user interface; best for custom solutions.<\/li>\n<li><a href=\"https:\/\/next-its.github.io\/\">NextITS<\/a> \u2013 metabarcoding data analyses pipeline for full-length ITS sequences from PacBio sequencers (integrated also in PipeCraft2).<\/li>\n<\/ul>\n<h2 dir=\"ltr\"><\/h2>\n<h2 dir=\"ltr\" style=\"text-align: justify;\">Other resources<\/h2>\n<ul>\n<li><a href=\"https:\/\/gsmc-fungi.github.io\/\">The Global Soil Mycobiome consortium (GSMc)<\/a> \u2013 global soil SSU-V9 + ITS dataset for all eukaryotes<\/li>\n<li><a href=\"https:\/\/link.springer.com\/article\/10.1007\/s13225-020-00466-2\">FungalTraits<\/a> ecological traits database for fungi and fungi-like stramenopiles<\/li>\n<li style=\"text-align: justify;\" role=\"presentation\"><a href=\"https:\/\/plutof.ut.ee\/\">PlutoF<\/a> \u2013 platform for metadata and taxonomic annotation and data curation<\/li>\n<li style=\"text-align: justify;\" role=\"presentation\"><a href=\"https:\/\/www.marinespecies.org\/\">WoRMS<\/a> \u2013 taxonomy and classification of marine biota<\/li>\n<li style=\"text-align: justify;\" role=\"presentation\"><a href=\"https:\/\/nemys.ugent.be\/\">NeMys<\/a> \u2013 ecological traits database for nematodes<\/li>\n<li style=\"text-align: justify;\" role=\"presentation\"><a href=\"https:\/\/unieuk.net\/\">UniEuk<\/a> \u2013 sequence and taxonomic resource for all eukaryotes, focus on marine protists<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Other databases Maintaining reference databases requires accurate and high-quality sequence data, as well as meticulous annotation and regular updates to reflect the rapidly expanding knowledge of bio diversity. Taxonomic annotation of sequencing data is provided in the following databases: UNITE &#8230;<\/p>\n","protected":false},"author":163,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"class_list":["post-15","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/15","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/users\/163"}],"replies":[{"embeddable":true,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/comments?post=15"}],"version-history":[{"count":3,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/15\/revisions"}],"predecessor-version":[{"id":478,"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/pages\/15\/revisions\/478"}],"wp:attachment":[{"href":"https:\/\/sisu.ut.ee\/eukaryome\/wp-json\/wp\/v2\/media?parent=15"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}