{"id":29223,"date":"2015-10-05T20:01:59","date_gmt":"2015-10-05T18:01:59","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-4-comparison-of-amino-acid-sequences\/"},"modified":"2021-06-17T18:13:34","modified_gmt":"2021-06-17T18:13:34","slug":"step-4-comparison-of-amino-acid-sequences","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-4-comparison-of-amino-acid-sequences\/?lang=sv","title":{"rendered":"Steg 4: J\u00e4mf\u00f6relse av aminosyrasekvenser"},"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-06938b10-94be-46c6-be96-2fffd279c159\">\u00d6versikt<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-8a733a57-5480-4758-911e-46ffc6af953b\">Din uppgift<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d194c45f-37fc-4601-8ab3-de9b4974a4a3\">MUSCLE<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-1285552d-049a-4c11-bd79-cfaa40a8f7a7\">Aminosyrasekvenser<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-7eb8e73c-ae74-4cfe-822f-3c7775beeee2\">Fr\u00e5gor<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-f9fcf67e-c0d4-45cc-b8bc-959d4ee50b10\">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-06938b10-94be-46c6-be96-2fffd279c159\"><h2>\u00d6versikt<\/h2>\n<p>I den h\u00e4r delen av aktiviteten ska vi ladda tv\u00e5 av proteinsekvenserna, som vi har genererat i det f\u00f6reg\u00e5ende steget, till EMBL-EBI MUSCLE alignment redskapet f\u00f6r att unders\u00f6ka likheten mellan dessa tv\u00e5 fluorescerande proteiner. En &#8220;sequence alignment&#8221; baserad p\u00e5 aminosyrasekvenser ger en starkare antydan av deras likheter j\u00e4mf\u00f6rt med en nukleotidsekvens. Denna &#8220;alignment&#8221; l\u00e5ter oss visualisera mutationer s\u00e5som addition, deletion eller utbyte inom aminosyrasekvenserna. Vi kan ocks\u00e5 finna aminosyrarester eller str\u00e4ckor som har konserverats starkt under evolutionen.<\/p>\n\n\n\n<p>Efter att ha genomf\u00f6rt den h\u00e4r uppgiften s\u00e5 har du producerat en &#8220;multiple sequence alignment&#8221; p\u00e5 proteinniv\u00e5 och du kommer att grovt kunna uppskatta var och vad skillnaderna mellan v\u00e5ra tv\u00e5 sekvenser \u00e4r.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-8a733a57-5480-4758-911e-46ffc6af953b\"><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 alla aminosyrasekvenser som erh\u00e5lls under fliken &#8220;Aminosyrasekvenser&#8221; (med andra ord markera och kopiera hela stycket med sekvenser) (genv\u00e4g Ctrl. + C).<\/li><li>Klistra in aminosyrasekvenserna i s\u00f6krutan i MUSCLE (genv\u00e4g Ctrl. + V).<\/li><li>F\u00f6lj instruktionerna under fliken &#8220;MUSCLE&#8221; f\u00f6r att &#8220;aligna&#8221; dina sekvenser.<\/li><li>Studera din &#8220;alignment&#8221; och f\u00f6rs\u00f6k besvara fr\u00e5gorna.<\/li><\/ol>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-d194c45f-37fc-4601-8ab3-de9b4974a4a3\"><h2>MUSCLE<\/h2>\n<ol class=\"wp-block-list\"><li>Kopiera alla aminosyrasekvenser som erh\u00e5lls under fliken &#8220;Aminosyrasekvenser&#8221; (med andra ord markera och kopiera hela stycket med sekvenser) (genv\u00e4g Ctrl. + C).<\/li><li>Klistra in aminosyrasekvenserna i s\u00f6krutan i MUSCLE (genv\u00e4g Ctrl. + V).<\/li><li>I &#8220;STEP 2&#8221; sektionen kolla att &#8220;<strong>Output Format<\/strong>&#8221; \u00e4r markerat vid <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 resultatet efter n\u00e5gra sekunder.<\/li><li>Studera din &#8220;alignment&#8221; och f\u00f6rs\u00f6k 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-1285552d-049a-4c11-bd79-cfaa40a8f7a7\"><h2>Aminosyrasekvenser<\/h2>\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nProtein sequence 1<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"><span style=\"word-break:break-all\"<\/span>&gt;Protein_Sequence1_AVGFP_1\nMSKGEELFTGVVPVLVELDGDVNGQKFSVSGEGEGDATYGKLTLNFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFYKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKMEYNYNSHNVYIMGDKPKNGIKVNFKIRHNIKDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMILLEFVTAARITHGMDELYK<\/pre>\n\n<\/div>\n<\/details>\n\n\n\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nProtein sequence 2<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"><span style=\"word-break:break-all\"<\/span>&gt;Protein_Sequence2_GFPm_1\nMSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK<\/pre>\n\n<\/div>\n<\/details>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-7eb8e73c-ae74-4cfe-822f-3c7775beeee2\"><h2>Fr\u00e5gor<\/h2>\n<p>Studera din protein &#8220;alignment&#8221; och f\u00f6rs\u00f6k besvara f\u00f6ljande fr\u00e5gor:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Hur vet du om aminosyrresterna i de enskilda sekvenserna \u00e4r desamma eller ej, j\u00e4mf\u00f6rt med de andra &#8220;alignade&#8221; sekvenserna?<\/li><li>Tycker du att det \u00e4r m\u00e5nga motsvarande aminosyror? \u00c4r det fler likheter j\u00e4mf\u00f6rt med respektive nukleotid &#8220;alignment&#8221;?<\/li><li>Vad tror du orsakerna \u00e4r till dessa f\u00f6r\u00e4ndringar?<\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-f9fcf67e-c0d4-45cc-b8bc-959d4ee50b10\"><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><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\">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\"><strong>Steg 5: GFP struktur<\/strong><\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":29224,"parent":28292,"menu_order":2,"template":"","class_list":["post-29223","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/29223","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\/29224"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=29223"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}