{"id":29167,"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":"2021-06-18T03:57:23","modified_gmt":"2021-06-18T03:57:23","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=it","title":{"rendered":"Step 2: Confronto di sequenze nucleotidiche"},"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\">Descrizione<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-78981bee-9962-4382-92d1-7136ffb3d4e5\">Il tuo compito<\/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\">Sequenze 1-4<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-9dfee51b-0a31-47d0-a3de-4ab80431fd4d\">Domande<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-c65f4728-e341-4de9-af06-7c0c71a681fe\">Liste attivita<\/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>Descrizione<\/h2>\n<p>Il confronto simultaneo di tutte le sequenze nucleotidiche pu\u00f2 essere ottenuto utilizzando il software web-based EMBL-EBI MUSCLE (Multiple Sequence Comparison by Log-Expectation). MUSCLE produce i cosiddetti <strong>sequence <\/strong><strong>alignments<\/strong>. Questi allineamenti possono essere utilizzati per visualizzare e interpretare le relazioni tra sequenze &#8211; e talvolta anche tra specie.<\/p>\n\n\n\n<p>Dopo aver completato questo esercizio avrete prodotto un allineamento multiplo di sequenze (a livello nucleotidico) e sarete in grado di determinare quali sequenze nucleotidiche sono maggiormente simili le une alle altre. le sequenze nucleotidiche (input) sono fornite nella tabulazione&#8221;Sequences&#8221;.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-78981bee-9962-4382-92d1-7136ffb3d4e5\"><h2>Il tuo compito<\/h2>\n<p><strong>Procedere come descritto sotto:<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Copiate tutte insieme le sequenze nucleotidiche fornite nella tabulazione &#8220;Sequences&#8221; (cio\u00e8 selezionate e copiate l&#8217;intero blocco di sequenze) (comando Ctrl. + C).<\/li><li>Incollate le sequenze nucleotidiche nel campo di ricerca MUSCLE (comando Ctrl. + V).<\/li><li>Seguite le istruzioni nella tabulazione &#8220;MUSCLE&#8221; per allineare le sequenze.<\/li><li>Osservate l&#8217;allineamento e cercate di rispondere alle domande nella tabulazione &#8220;Questions&#8221;.<\/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>Copiate tutte insieme le sequenze nucleotidiche fornite nella tabulazione &#8220;Sequences&#8221; (cio\u00e8 selezionate e copiate l&#8217;intero blocco di sequenze) (comando Ctrl. + C).<\/li><li>Incollate le sequenze nucleotidiche nel campo di ricerca MUSCLE (comando Ctrl. + V).<\/li><li>Nella sezione &#8220;STEP 2&#8221; assicurtevi che &#8220;<strong>Output Format<\/strong>&#8221; sia su <strong>&#8220;ClustalW&#8221;<\/strong>.<\/li><li>Cliccare sul grande bottone <strong>&#8220;Submit<\/strong>&#8221; e il vostro allineamento verr\u00e0 elaborato.<\/li><li>I risultati appariranno dopo pochi secondi. Osservate l&#8217;allineamento e cercate di rispondere alle domande nella tabulazione &#8220;Questions&#8221;.<\/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>Sequenze 1-4<\/h2>\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSequenza 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\">\nSequenza 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\">\nSequenza 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\">\nSequenza 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>Domande<\/h2>\n<p><strong>Procedere come descritto sotto:<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Copiate tutte insieme le sequenze nucleotidiche fornite nella tabulazione \u201cSequences\u201d (cio\u00e8 selezionate e copiate l\u2019intero blocco di sequenze) (comando Ctrl. + C).<\/li><li>Incollate le sequenze nucleotidiche nel campo di ricerca MUSCLE (comando Ctrl. + V).<\/li><li>Seguite le istruzioni nella tabulazione \u201cMUSCLE\u201d per allineare le sequenze.<\/li><li>Osservate l\u2019allineamento e cercate di rispondere alle domande nella tabulazione \u201cQuestions\u201d.<\/li><\/ol>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-c65f4728-e341-4de9-af06-7c0c71a681fe\"><h2>Liste attivita<\/h2>\n<p><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/?lang=it\">Caccia al tesoro GFP<\/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=it\">Caccia al tesoro GFP \u2013 Introduzione<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/?lang=it\">Step 1: Ricerca nel database<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-2-comparison-of-nucleotide-sequences\/?lang=it\">Step 2: Confronto di sequenze nucleotidiche<\/a><\/li><li><strong><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-3-translation-of-mrnas\/?lang=it\">Step 3: Traduzione degli mRNA<\/a><\/strong><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-4-comparison-of-amino-acid-sequences\/?lang=it\">Step 4: Confronto di sequenze aminoacidiche<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-5-structure-of-gfp\/?lang=it\">Step 5: Struttura della GFP<\/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":29168,"parent":28290,"menu_order":4,"template":"","class_list":["post-29167","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/29167","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\/28290"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/29168"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=29167"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}