{"id":29169,"date":"2015-10-05T19:36:46","date_gmt":"2015-10-05T17:36:46","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-2-comparison-of-nucleotide-sequences\/"},"modified":"2021-06-18T03:48:01","modified_gmt":"2021-06-18T03:48:01","slug":"step-2-comparison-of-nucleotide-sequences","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-2-comparison-of-nucleotide-sequences\/?lang=sv","title":{"rendered":"Steg 2: J\u00e4mf\u00f6relse av nukleotidsekvenser"},"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-da0d437d-5f99-4d34-b6fa-c991f58a5130\">\u00d6versikt<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-78981bee-9962-4382-92d1-7136ffb3d4e5\">Din uppgift<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-9c0782e4-2aaa-4390-accc-3ea3048a359c\">MUSCLE<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d8ee530d-eb3f-41b4-9c68-04224aba4a8f\">Sekvenser 1-4<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-9dfee51b-0a31-47d0-a3de-4ab80431fd4d\">Fr\u00e5gor<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-c65f4728-e341-4de9-af06-7c0c71a681fe\">Activity navigation<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-da0d437d-5f99-4d34-b6fa-c991f58a5130\"><h2>\u00d6versikt<\/h2>\n<p>En samtidig j\u00e4mf\u00f6relse av alla dina nukleotidsekvenser kan g\u00f6ras genom att anv\u00e4nda den server-baserade mjukvaran EMBL-EBI MUSCLE (Multiple Sequence Comparison by Log-Expectation). MUSCLE producerar s\u00e5 kallade <strong>sequence <\/strong><strong>alignments<\/strong>. Dessa &#8220;alignments&#8221; kan anv\u00e4ndas f\u00f6r att visualisera och tolka sambanden mellan sekvenser \u2013 och ibland \u00e4ven mellan arter.<\/p>\n\n\n\n<p>N\u00e4r du \u00e4r klar med den h\u00e4r \u00f6vningen s\u00e5 har du gjort en &#8220;multiple sequence alignment&#8221; (p\u00e5 nukleotid niv\u00e5) och kan grovt bed\u00f6ma vilka nukleotidsekvenser som \u00e4r mest lika varandra. Nukleotidsekvenserna (inf\u00f6rda) tillhandah\u00e5lls i fliken &#8220;Sekvenser&#8221;.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-78981bee-9962-4382-92d1-7136ffb3d4e5\"><h2>Din uppgift<\/h2>\n<p><strong>Forts\u00e4tt som beskrivs nedan:<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Kopiera omg\u00e5ende samtliga nukleotidsekvenser som tillhandah\u00e5lls i fliken &#8220;Sekvenser&#8221; (med andra ord markera och kopiera hela stycket med sekvenser) (genv\u00e4g Ctrl. + C).<\/li><li>Klistra in nukleotidsekvenserna i s\u00f6krutan i MUSCLE (genv\u00e4g Ctrl. + V).<\/li><li>F\u00f6lj instruktionerna i fliken &#8220;MUSCLE&#8221; f\u00f6r att &#8220;aligna&#8221; dina sekvenser.<\/li><li>Titta p\u00e5 din &#8220;alignment&#8221; och f\u00f6rs\u00f6k att besvara fr\u00e5gorna i &#8220;Fr\u00e5gor&#8221; fliken.<\/li><\/ol>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-9c0782e4-2aaa-4390-accc-3ea3048a359c\"><h2>MUSCLE<\/h2>\n<ol class=\"wp-block-list\"><li>Kopiera omg\u00e5ende samtliga nukleotidsekvenser som tillhandah\u00e5lls i fliken &#8220;Sekvenser&#8221; (med andra ord markera och kopiera hela stycket med sekvenser) (genv\u00e4g Ctrl. + C).<\/li><li>Klistra in nukleotidsekvenserna i s\u00f6krutan i MUSCLE (genv\u00e4g Ctrl. + V).<\/li><li>I &#8220;STEP 2&#8221; sektionen kollar du att &#8220;<strong>Output Format<\/strong>&#8221; \u00e4r inst\u00e4llt p\u00e5 <strong>&#8220;ClustalW&#8221;<\/strong>.<\/li><li>Klicka p\u00e5 den stora <strong>&#8220;Submit<\/strong>&#8221; knappen och din &#8220;alignment&#8221; kommer att behandlas.<\/li><li>Du ser dina resultat efter ett par sekunder. Titta p\u00e5 din &#8220;alignment&#8221; och f\u00f6rs\u00f6k att besvara fr\u00e5gorna i &#8220;Fr\u00e5gor&#8221; fliken.<\/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\/Tools\/msa\/muscle\/\" 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-d8ee530d-eb3f-41b4-9c68-04224aba4a8f\"><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>&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-9dfee51b-0a31-47d0-a3de-4ab80431fd4d\"><h2>Fr\u00e5gor<\/h2>\n<p>Titta p\u00e5 din &#8220;alignment&#8221; och f\u00f6rs\u00f6k att besvara f\u00f6ljande fr\u00e5gor:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Hur vet du om nukleotiderna i de enskilda sekvenserna \u00e4r detsamma eller ej, j\u00e4mf\u00f6rt med de andra &#8220;alignade&#8221; sekvenserna?<\/li><li>Tror du att det finns m\u00e5nga motsvarande nukleotider? Skulle du ha f\u00f6rv\u00e4ntat dig n\u00e5got annat?<\/li><li>Vilka av de tv\u00e5 sekvenserna bed\u00f6mer du som mest lika varandra?<\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-c65f4728-e341-4de9-af06-7c0c71a681fe\"><h2>Activity navigation<\/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><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><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-3-translation-of-mrnas\/?lang=sv\"><strong>Steg 3: Translation av mRNA<\/strong><\/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\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":29170,"parent":28292,"menu_order":4,"template":"","class_list":["post-29169","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/29169","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\/29170"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=29169"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}