{"id":29178,"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":"2021-06-18T04:11:02","modified_gmt":"2021-06-18T04:11:02","slug":"step-1-database-search","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/?lang=cs","title":{"rendered":"Krok 1: Vyhled\u00e1v\u00e1n\u00ed v datab\u00e1zi"},"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\">\u00davod<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d751d2a3-18f5-4d42-8d6c-d40e16241457\">Va\u0161e \u00faloha<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-9b3f966e-eb04-4603-b78b-09e591f90152\">ENA<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-9f84c97d-209d-4748-b6c9-776638207dba\">Sekvence 1-4<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-52c6bc99-9a02-4ae5-8a6e-430840bb6818\">Ot\u00e1zky<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-57c18e1e-283c-432a-a483-35a065748008\">Navigace aktivity<\/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>\u00davod<\/h2>\n<p>P\u0159edstavte si, \u017ee va\u0161e vzorky DNA se p\u0159ed odesl\u00e1n\u00edm do sekvena\u010dn\u00edho centra omylem pom\u00edchaly a my te\u010f nev\u00edme, kter\u00fd je kter\u00fd. Abychom znovu ur\u010dili jejich p\u016fvodn\u00ed toto\u017enost, prohled\u00e1me nukleotidovou datab\u00e1zi zvanou European Nucleotide Archive (ENA).<\/p>\n\n\n\n<p>Sekvence, kter\u00e9 chceme analyzovat, naleznete v z\u00e1lo\u017ece \u201cSekvence\u201d. Ka\u017ed\u00e1 z nich m\u00e1 pouze velmi obecn\u00fd n\u00e1zev, ale po prohled\u00e1n\u00ed ENA byste m\u011bli b\u00fdt schopni ozna\u010dit sekvence prav\u00fdm jm\u00e9nem a ur\u010dit organismus, ze kter\u00e9ho poch\u00e1zej\u00ed.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-d751d2a3-18f5-4d42-8d6c-d40e16241457\"><h2>Va\u0161e \u00faloha<\/h2>\n<p><strong><strong>Postupujte n\u00e1sledovn\u011b:<\/strong><\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Jd\u011bte do z\u00e1lo\u017eky &#8220;Sekvence 1&#8221; a zkop\u00edrujte celou sekvenci v\u010detn\u011b identifik\u00e1toru &#8220;&gt;Sequence 1&#8221; (pro zkop\u00edrov\u00e1n\u00ed pou\u017eijte Ctrl.+C).<\/li><li>\u0158i\u010fte se pokyny v z\u00e1lo\u017ece &#8220;ENA&#8221;.<\/li><li>Zaznamenejte si, co jste na\u0161li a pokuste se odpov\u011bd\u011bt na ot\u00e1zky v z\u00e1lo\u017ece &#8220;Ot\u00e1zky&#8221;. Stejn\u011b postupujte i se zbytkem sekvenc\u00ed.<\/li><\/ol>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-9b3f966e-eb04-4603-b78b-09e591f90152\"><h2>ENA<\/h2>\n<ol class=\"wp-block-list\"><li>Vlo\u017ete sekveci do vstupn\u00edho okna programu ENA (pomoc\u00ed Ctrl.+V).<\/li><li>Nyn\u00ed klikn\u011bte na <strong>&#8220;Submit&#8221;<\/strong> dole na str\u00e1nce, \u010d\u00edm\u017e zah\u00e1j\u00edte prohled\u00e1v\u00e1n\u00ed datab\u00e1ze. V\u00e1mi vlo\u017een\u00e1 sekvence je porovn\u00e1v\u00e1na se v\u0161emi sekvencemi p\u0159itomn\u00fdmi v datab\u00e1zi.<\/li><li>Za n\u011bkolik sekund se objev\u00ed v\u00fdsledky. Projd\u011bte str\u00e1nku v\u00fdsledk\u016f a ve sloupe\u010dc\u00edch ozna\u010den\u00fdch &#8220;ENA&#8221; se pokuste naj\u00edt, sekvence kter\u00e9ho biologick\u00e9ho druhu byla nalezena jako nejpodobn\u011bj\u0161\u00ed na\u0161\u00ed nezn\u00e1m\u00e9 sekvenci. Nejpodobn\u011bj\u0161\u00ed sekvence maj\u00ed &#8220;Identity (%)&#8221; rovnou 100 a &#8220;E-Value&#8221; rovnu 0.<\/li><li>Zaznamenejte si, co jste na\u0161li a pokuste se odpov\u011bd\u011bt na ot\u00e1zky v z\u00e1lo\u017ece &#8220;Ot\u00e1zky&#8221;. Stejn\u011b postupujte i se zbytkem sekvenc\u00ed.<\/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>Sekvence 1-4<\/h2>\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSekvence 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\">\nSekvence 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\">\nSekvence 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\">\nSekvence 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>Ot\u00e1zky<\/h2>\n<ul class=\"wp-block-list\"><li>Kter\u00e9 biologick\u00e9 druhy odpov\u00eddaj\u00ed sekvenc\u00edm 1, 2, 3 a 4?<\/li><li>Pod\u00edv\u00e1te-li se na v\u00fdsledky &#8220;Alignments&#8221;, m\u016f\u017eete si zobrazit i vz\u00e1jemn\u00e9 (1:1) porovn\u00e1n\u00ed dvou sekvenc\u00ed. Toto se naz\u00fdv\u00e1 &#8220;pairwise alignment&#8221; (p\u00e1rov\u00e9 porovn\u00e1n\u00ed) a zobraz\u00edte ho tak, \u017ee bu\u010f kliknete na v\u00fdsledky jednotliv\u00fdch porovn\u00e1n\u00ed, nebo &#8220;Show all alignments&#8221; dole na str\u00e1nce v\u00fdsledk\u016f ENA.<ul><li>Jak jsou ozna\u010deny nukleotidy, kter\u00e9 jsou shodn\u00e9 v obou sekvenc\u00edch?<\/li><li>Porovnejte va\u0161i p\u016fvodn\u00ed sekvenc\u00ed se sekvenc\u00ed z datab\u00e1ze. Najdete mnoho rozd\u00edl\u016f?<\/li><li>Najdete rozd\u00edly mezi jednotliv\u00fdmi nukleotidy ve dvou porovnan\u00fdch sekvenc\u00edch? Napadaj\u00ed v\u00e1s d\u016fvody pro\u010d tomu tak je?<\/li><\/ul><\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-57c18e1e-283c-432a-a483-35a065748008\"><h2>Navigace aktivity<\/h2>\n<p><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/?lang=cs\">Honba za pokladem &#8211; 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=cs\">Honba za pokladem &#8211; GFP &#8211; \u00favod<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/?lang=cs\">Krok 1: Vyhled\u00e1v\u00e1n\u00ed v datab\u00e1zi<\/a><\/li><li><strong><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-2-comparison-of-nucleotide-sequences\/?lang=cs\">Krok 2: Porovn\u00e1n\u00ed nukleotidov\u00fdch sekvenc\u00ed<\/a><\/strong><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-3-translation-of-mrnas\/?lang=cs\">Krok 3: P\u0159eklad mRNA<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-4-comparison-of-amino-acid-sequences\/?lang=cs\">Krok 4: Srovn\u00e1n\u00ed aminokyselinov\u00fdch sekvenc\u00ed<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-5-structure-of-gfp\/?lang=cs\">Krok 5: Struktura proteinu GFP<\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":29179,"parent":28284,"menu_order":5,"template":"","class_list":["post-29178","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/29178","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\/28284"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/29179"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=29178"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}