{"id":29184,"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":"2021-06-18T03:58:15","modified_gmt":"2021-06-18T03:58:15","slug":"step-1-database-search","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/?lang=it","title":{"rendered":"Step 1: Ricerca nel database"},"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\">Descrizione<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d751d2a3-18f5-4d42-8d6c-d40e16241457\">Il tuo compito<\/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\">Sequenze 1-4<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-52c6bc99-9a02-4ae5-8a6e-430840bb6818\">Domande<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-04d3c583-1429-4e21-8a61-af4feccc3249\">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-eb3017af-9360-4832-908c-107a9f99818b\"><h2>Descrizione<\/h2>\n<p>Immaginate che i nostri campioni di DNA siano stati mescolati prima del sequenziamento e che non sappiamo chi corrisponde a chi. Per stabilire l&#8217;identit\u00e0 delle sequenze e sapere qualcosa sulle loro origini, condurremo una ricerca sul database European Nucleotide Archive (ENA).<\/p>\n\n\n\n<p>Le sequenze che utilizzeremo per la nostra analisi si trovano nella tabulazione &#8220;Sequences&#8221; qui sotto. Ognuna ha un nome generico, e dopo la ricerca nel database ENA sarete in grado di assegnare le sequenze ai quattro organismi a cui appartengono.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-d751d2a3-18f5-4d42-8d6c-d40e16241457\"><h2>Il tuo compito<\/h2>\n<p><strong>Procedere come descritto sotto:<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Aprite la tabulazione &#8220;Sequence 1&#8221; e copiate l&#8217;intera sequenza che inizia con &#8220;&gt;Sequence 1&#8221;. Potete usare il comando da tastiera Ctrl.+C per copiare la sequenza.<\/li><li>Seguite le istruzioni nella tabulazione &#8220;ENA&#8221; per fare la ricerca nel database.<\/li><li>Annotate quello che avete trovato, provate a rispondere alle domande nella tabulazione &#8220;Questions&#8221; e ripetete questo procedimento con le altre sequenze.<\/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>Incollate la sequenza nel campo di ricerca ENA (comando Ctrl.+V).<\/li><li>Ora, cliccate su <strong>&#8220;Submit<\/strong><strong>&#8220;<\/strong> in basso e la ricerca avr\u00e0 inizio. La sequenza che avete inserito sar\u00e0 paragonata a tutte le sequenze note contenute nel database.<\/li><li>I risultati della ricerca appariranno dopo pochi secondi. Scorrete la pagina fino alle colonne intestate &#8220;ENA&#8221; e cercate di scoprire quali sono le specie che corrispondono alla vostra sequenza identificate dalla ricerca. Le sequenze pi\u00f9 simili hanno un valore &#8220;Identity (%)&#8221; di 100 e un &#8220;E-Value&#8221; di 0.<\/li><li>Annotate quello che avete trovato, provate a rispondere alle domande nella tabulazione &#8220;Questions&#8221; e ripetete questo procedimento con le altre sequenze.<\/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>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>\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\">\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-52c6bc99-9a02-4ae5-8a6e-430840bb6818\"><h2>Domande<\/h2>\n<ul class=\"wp-block-list\"><li>A quali specie corrispondono le sequenze 1, 2, 3 e 4?<\/li><li>Osservando &#8220;Alignments&#8221; troverete un confronto 1:1 delle due sequenze. Questo \u00e8 chiamato un &#8220;pairwise alignment&#8221;. Per vedere gli allineamenti, potete cliccare sulla descrizione del singolo risultato della ricerca o cliccare su &#8220;Show all alignments&#8221; in basso nei risultati ENA.<ul><li>Come sono rappresentati i nucleotidi che si corrispondono nelle due sequenze?<\/li><li>Confrontate la vostra sequenza iniziale con la sequenza del database. Ci sono differenze tra la vostra sequenza (query) e la sequenza archiviata nel database (subject)?<\/li><li>Ci sono differenze a livello di singoli nucleotidi tra le due sequenze? Quale potrebbe essere il motivo?<\/li><\/ul><\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-04d3c583-1429-4e21-8a61-af4feccc3249\"><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\"><strong>Step 2: Confronto di sequenze nucleotidiche<\/strong><\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-3-translation-of-mrnas\/?lang=it\">Step 3: Traduzione degli mRNA<\/a><\/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","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":29185,"parent":28290,"menu_order":5,"template":"","class_list":["post-29184","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/29184","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\/29185"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=29184"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}