{"id":29186,"date":"2015-10-05T19:30:56","date_gmt":"2015-10-05T17:30:56","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/"},"modified":"2021-06-18T03:48:45","modified_gmt":"2021-06-18T03:48:45","slug":"step-1-database-search","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/?lang=sv","title":{"rendered":"Steg 1: Databas s\u00f6kning"},"content":{"rendered":"\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-eb3017af-9360-4832-908c-107a9f99818b\">\u00d6versikt<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d751d2a3-18f5-4d42-8d6c-d40e16241457\">Din uppgift<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d3b43fe3-023d-481e-afb7-6734f27d7e1d\">ENA<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-9f84c97d-209d-4748-b6c9-776638207dba\">Sekvenser 1-4<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-52c6bc99-9a02-4ae5-8a6e-430840bb6818\">Fr\u00e5gor<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-8a08190e-8d17-4c24-a88a-801893213516\">Aktivitetsnavigering<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-eb3017af-9360-4832-908c-107a9f99818b\"><h2>\u00d6versikt<\/h2>\n<p>F\u00f6rest\u00e4ll dig att v\u00e5ra DNA-prover har blandats innan sekvensering och vi vet inte vilket prov som \u00e4r vilket. F\u00f6r att fastst\u00e4lla sekvensernas identitet och ta reda p\u00e5 mera om deras ursprung, s\u00e5 kommer vi att genomf\u00f6ra en s\u00f6kning i en databas som kallas European Nucleotide Archive (ENA).<\/p>\n\n\n\n<p>Sekvenserna som vi ska anv\u00e4nda f\u00f6r v\u00e5r analys finns nedan i &#8220;Sekvens&#8221; flikarna. Var och en av dem har ett sl\u00e4ktnamn, och efter ENA s\u00f6kningen ska du kunna tilldela sekvenserna till ursprunget f\u00f6r fyra organismer.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-d751d2a3-18f5-4d42-8d6c-d40e16241457\"><h2>Din uppgift<\/h2>\n<p><strong>Forts\u00e4tt som beskrivs nedan:<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>G\u00e5 till fliken &#8220;Sekvens 1&#8221; och kopiera hela sekvensen som startar med &#8220;&gt;Sequence 1&#8221;. Du kan anv\u00e4nda genv\u00e4gen Ctrl.+C p\u00e5 tangentbordet f\u00f6r att kopiera sekvensen.<\/li><li>F\u00f6lj instruktionerna i &#8220;ENA&#8221; fliken f\u00f6r att s\u00f6ka i databasen.<\/li><li>Notera vad du har funnit, f\u00f6rs\u00f6k besvara fr\u00e5gorna i &#8220;Fr\u00e5gor&#8221; fliken och upprepa proceduren med resten av sekvenserna.<\/li><\/ol>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-d3b43fe3-023d-481e-afb7-6734f27d7e1d\"><h2>ENA<\/h2>\n<ol class=\"wp-block-list\"><li>Klistra in sekvensen i ENA-s\u00f6krutan (genv\u00e4g Ctrl.+V).<\/li><li>Klicka p\u00e5 <strong>&#8220;Submit<\/strong><strong>&#8220;<\/strong> l\u00e4ngst ned och din s\u00f6kning kommer att p\u00e5b\u00f6rjas. Den infogade sekvensen kommer nu att j\u00e4mf\u00f6ras med alla k\u00e4nda sekvenser som finns i databasen.<\/li><li>Du f\u00e5r s\u00f6kresultaten presenterade efter n\u00e5gra sekunder. Skrolla genom sidan till kolumnerna med rubriken &#8220;ENA&#8221; och f\u00f6rs\u00f6k lista ut vilken art som identifierades f\u00f6r att matcha din sekvens. De mest liknande sekvenserna har en &#8220;Identity (%)&#8221; v\u00e4rde som \u00e4r 100 och ett &#8220;E-Value&#8221; som \u00e4r 0.<\/li><li>Notera vad du har funnit, f\u00f6rs\u00f6k besvara fr\u00e5gorna i &#8220;Fr\u00e5gor&#8221; fliken och upprepa proceduren med resten av sekvenserna.<\/li><\/ol>\n\n\n<div\n  class=\"vf-embed vf-embed--custom-ratio\"\n\n  style=\"--vf-embed-max-width: 100%;\n    --vf-embed-custom-ratio-x: 640;\n    --vf-embed-custom-ratio-y: 360;\"\n><iframe loading=\"lazy\" width=\"640\" height=\"360\" src=\"https:\/\/www.ebi.ac.uk\/ena\/browser\/\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-9f84c97d-209d-4748-b6c9-776638207dba\"><h2>Sekvenser 1-4<\/h2>\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSekvens 1<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"><span style=\"word-break:break-all\"<\/span>&gt;Sequence1_AVGFP\nATGAGTAAAGGAGAAGAACTTTTCACTGGAGTGGTCCCAGTTCTTGTTGAATTAGATGGCGATGTTAATGGGCAAAAATTCTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACATACGGAAAACTTACCCTTAATTTTATTTGCACTACTGGGAAGCTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTCTCAAGATACCCAGATCATATGAAACAGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAAAGAACTATATTTTACAAAGATGACGGGAACTACAAGACACGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATAGAATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAAATGGAATACAACTATAACTCACATAATGTATACATCATGGGAGACAAACCAAAGAATGGCATCAAAGTTAACTTCAAAATTAGACACAACATTAAAGATGGAAGCGTTCAATTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCCAAAGATCCCAACGAAAAGAGAGATCACATGATCCTTCTTGAGTTTGTAACAGCTGCTAGGATTACACATGGCATGGATGAACTATACAAA<\/pre>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSekvens 2<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"><span style=\"word-break:break-all\"<\/span>\n&gt;Sequence2_GFPm\nATGTCTAAAGGTGAAGAATTATTCACTGGTGTTGTCCCAATTTTGGTTGAATTAGATGGTGATGTTAATGGTCACAAATTTTCTGTCTCCGGTGAAGGTGAAGGTGATGCTACTTACGGTAAATTGACCTTAAAATTTATTTGTACTACTGGTAAATTGCCAGTTCCATGGCCAACCTTAGTCACTACTTTCGGTTATGGTGTTCAATGTTTTGCTAGATACCCAGATCATATGAAACAACATGACTTTTTCAAGTCTGCCATGCCAGAAGGTTATGTTCAAGAAAGAACTATTTTTTTCAAAGATGACGGTAACTACAAGACCAGAGCTGAAGTCAAGTTTGAAGGTGATACCTTAGTTAATAGAATCGAATTAAAAGGTATTGATTTTAAAGAAGATGGTAACATTTTAGGTCACAAATTGGAATACAACTATAACTCTCACAATGTTTACATCATGGCTGACAAACAAAAGAATGGTATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGTTCTGTTCAATTAGCTGACCATTATCAACAAAATACTCCAATTGGTGATGGTCCAGTCTTGTTACCAGACAACCATTACTTATCCACTCAATCTGCCTTATCCAAAGATCCAAACGAAAAGAGAGACCACATGGTCTTGTTAGAATTTGTTACTGCTGCTGGTATTACCCATGGTATGGATGAATTGTACAAATAACTGCAG<\/pre>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSekvens 3<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"><span style=\"word-break:break-all\"<\/span>&gt;Sequence3_YFP\nAATATTTTTATTAATTCATTAGAAAAATGAGAGGAAGGATTATTATGTTTAAAGGTATAGTAGAAGGTATAGGAATCATTGAAAAAATTGATATATATACTGACCTAGATAAGTATGCAATTCGATTTCCTGAAAATATGTTGAATGGAATTAAAAAGGAGTCGTCAATAATGTTTAACGGATGCTTCTTAACGGTAACTAGCGTGAATTCAAACATTGTCTGGTTTGATATATTTGAAAAAGAAGCACGTAAGCTTGATACTTTTCGGGAATATAAGGTAGGTGACCGAGTAAATTTAGGAACATTCCCAAAATTTGGCGCTGCATCTGGTGGGCATATATTATCAGCAAGGATTTCATGTGTAGCAAGTATTATTGAAATAATAGAAAATGAGGATTATCAACAAATGTGGATTCAAATTCCTGAAAATTTTACAGAGTTTCTTATTGATAAAGACTATATTGCTGTGGATGGTATTAGCTTAACTATTGACACTATAAAAAACAACCAATTTTTCATTAGTTTACCCTTAAAAATAGCACAAAATACAAATATGAAATGGCGAAAAAAAGGTGATAAGGTAAATGTTGAGTTATCAAACAAAATTAATGCTAACCAGTGTTGGTAATTTACTGAGGATAGTAAAAATGAACTGTTTAAAATAATATTTAAATTTTTATTTATAATACAGAGTCAGTTGTTGTAAATAGTCTGAGTGGTAAATAAGTTCTACCATTAATTAAATATTATCCATATTAAATAAAGGATCT<\/pre>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSekvens 4<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"><span style=\"word-break:break-all\"<\/span>&gt;Sequence4_RFP\nAGTTTCAGCCAGTGACAGGGTGAGCTGCCAGGTATTCTAACAAGATGAGTTGTTCCAAGAATGTGATCAAGGAGTTCATGAGGTTCAAGGTTCGTATGGAAGGAACGGTCAATGGGCACGAGTTTGAAATAAAAGGCGAAGGTGAAGGGAGGCCTTACGAAGGTCACTGTTCCGTAAAGCTTATGGTAACCAAGGGTGGACCTTTGCCATTTGCTTTTGATATTTTGTCACCACAATTTCAGTATGGAAGCAAGGTATATGTCAAACACCCTGCCGACATACCAGACTATAAAAAGCTGTCATTTCCTGAGGGATTTAAATGGGAAAGGGTCATGAACTTTGAAGACGGTGGCGTGGTTACTGTATCCCAAGATTCCAGTTTGAAAGACGGCTGTTTCATCTACGAGGTCAAGTTCATTGGGGTGAACTTTCCTTCTGATGGACCTGTTATGCAGAGGAGGACACGGGGCTGGGAAGCCAGCTCTGAGCGTTTGTATCCTCGTGATGGGGTGCTGAAAGGAGACATCCATATGGCTCTGAGGCTGGAAGGAGGCGGCCATTACCTCGTTGAATTCAAAAGTATTTACATGGTAAAGAAGCCTTCAGTGCAGTTGCCAGGCTACTATTATGTTGACTCCAAACTGGATATGACGAGCCACAACGAAGATTACACAGTCGTTGAGCAGTATGAAAAAACCCAGGGACGCCACCATCCGTTCATTAAGCCTCTGCAGTGAACTCGGCTCAGTCATGGATTAGCGGTAATGGCCACAAAAGGCACGATGATCGTTTTTTAGGAATGCAGCCAAAAATTGAAGGTTATGACAGTAGAAATACAAGCAACAGGCTTTGCTTATTAAACATGTAATTGAAAAC<\/pre>\n\n<\/div>\n<\/details>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-52c6bc99-9a02-4ae5-8a6e-430840bb6818\"><h2>Fr\u00e5gor<\/h2>\n<ul class=\"wp-block-list\"><li>Vilka arter kan knytas till sekvenserna 1, 2, 3 and 4?<\/li><li>Titta p\u00e5 &#8220;Alignments&#8221; och du ser en 1:1 j\u00e4mf\u00f6relse av de tv\u00e5 sekvenserna. Detta kallas f\u00f6r &#8220;pairwise alignment&#8221;. F\u00f6r att se denna &#8220;alignment&#8221;, antingen klicka p\u00e5 beskrivningen av varje enskilt s\u00f6kresultat eller klicka p\u00e5 &#8220;Show all alignments&#8221; l\u00e4ngst ned i ENA resultaten.<ul><li>Hur framst\u00e4lls nukleotiderna som matchas i b\u00e5da sekvenserna?<\/li><li>J\u00e4mf\u00f6r din inmatade sekvens med databas-sekvensen. Finns n\u00e5gra skillnader mellan din sekvens (query) och sekvensen som lagrats i databasen (subject)?<\/li><li>Finns n\u00e5gra skillnader mellan enskilda nukleotider i de tv\u00e5 sekvenserna? Vad kan det bero p\u00e5?<\/li><\/ul><\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-8a08190e-8d17-4c24-a88a-801893213516\"><h2>Aktivitetsnavigering<\/h2>\n<p><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/?lang=sv\">GFP skattjakt<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/gfp-treasure-hunt-introduction\/?lang=sv\">GFP skattjakt introduktion<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/?lang=sv\">Steg 1: Databas s\u00f6kning<\/a><\/li><li><strong><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-2-comparison-of-nucleotide-sequences\/?lang=sv\">Steg 2: J\u00e4mf\u00f6relse av nukleotidsekvenser<\/a><\/strong><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-3-translation-of-mrnas\/?lang=sv\">Steg 3: Translation av mRNA<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-4-comparison-of-amino-acid-sequences\/?lang=sv\">Steg 4: J\u00e4mf\u00f6relse av aminosyrasekvenser<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-5-structure-of-gfp\/?lang=sv\">Steg 5: GFP struktur<\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":29187,"parent":28292,"menu_order":5,"template":"","class_list":["post-29186","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/29186","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase"}],"about":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/types\/teachingbase"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28292"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/29187"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=29186"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}