{"id":28284,"date":"2014-04-24T09:34:56","date_gmt":"2014-04-24T07:34:56","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/"},"modified":"2021-06-18T14:51:53","modified_gmt":"2021-06-18T14:51:53","slug":"gfp-treasure-hunt","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/?lang=cs","title":{"rendered":"Honba za pokladem \u2013 GFP"},"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-523c3925-2c9f-4e6a-bdd1-5bd70abac03c\">\u00davod<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-12bcdfb5-2c34-4290-915e-92e21cc545e1\">Technick\u00e9 po\u017eadavky<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-be0af349-8cc4-4a10-916c-28f87a4b1f8a\">Bioinformatick\u00e9 n\u00e1stroje<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-5498d92f-f4cd-41e3-94ef-bfd891b4e6a4\">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-523c3925-2c9f-4e6a-bdd1-5bd70abac03c\"><h2>\u00davod<\/h2>\n<p>Tato \u00faloha \u201chonba za pokladem\u201d byla navr\u017eena tak, aby v\u00e1s sezn\u00e1mila s r\u016fzn\u00fdmi bioinformatick\u00fdmi postupy, pomoc\u00ed kter\u00fdch m\u016f\u017eete identifikovat a analyzovat sekvence DNA a protein\u016f. V t\u00e9to \u00faloze budeme analyzovat sekvence zelen\u00e9ho fluorescen\u010dn\u00edho proteinu&nbsp; (Green Fluorescent Protein \u2013 GFP) a jemu p\u0159\u00edbuzn\u00fdch molekul pomoc\u00ed online bioinformatick\u00fdch n\u00e1stroj\u016f a datab\u00e1z\u00ed. Biologick\u00e1 data, nap\u0159. DNA a proteinov\u00e9 sekvence a strukturn\u00ed infomace jsou ukl\u00e1d\u00e1ny v datab\u00e1z\u00edch, kter\u00e9 jsou udr\u017eov\u00e1ny a ur\u010deny pro v\u011bdeckou pr\u00e1ci. Proto\u017ee v\u0161ak je v\u011bt\u0161ina t\u011bchto dat vytv\u00e1\u0159ena pomoc\u00ed ve\u0159ejn\u00fdch pen\u011bz v podob\u011b grant\u016f atd., jsou tyto datab\u00e1ze dostupn\u00e9 ka\u017ed\u00e9mu. Stejn\u011b tak jsou bioinformatick\u00e9 n\u00e1stroje vytv\u00e1\u0159en\u00e9 v\u011bdeckou komunitou voln\u011b dostupn\u00e9 pro \u0161irokou ve\u0159ejnost. V na\u0161em kurzu budeme po celou dobu pou\u017e\u00edvat tyto voln\u011b dostupn\u00e9 zdroje a n\u00e1stroje.<br>N\u00ed\u017ee uveden\u00e9 naviga\u010dn\u00ed menu obsahuje jednotliv\u00e9 kroky prvn\u00ed \u00falohy. Za\u010dn\u011bte va\u0161i \u201chonbu za pokladem\u201d kliknut\u00edm na \u201cHonba za pokladem \u2013 GFP \u2013 \u00favod\u201d.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-12bcdfb5-2c34-4290-915e-92e21cc545e1\"><h2>Technick\u00e9 po\u017eadavky<\/h2>\n<p>Pro pou\u017e\u00edv\u00e1n\u00ed program\u016f JalView a Astex Viewer je zapot\u0159eb\u00ed m\u00edt v po\u010d\u00edta\u010di nainstalovanou Javu a Java mus\u00ed b\u00fdt rovn\u011b\u017e povolena v internetov\u00e9m prohl\u00ed\u017ee\u010di. Javu m\u016f\u017eete zdarma nainstalovat pomoc\u00ed&nbsp;<a rel=\"noreferrer noopener\" href=\"http:\/\/www.java.com\/en\/\" target=\"_blank\">java.com<\/a>. Informace jak povolit Javu ve va\u0161em prohl\u00ed\u017ee\u010di najdete&nbsp;<a rel=\"noreferrer noopener\" href=\"http:\/\/www.java.com\/en\/\" target=\"_blank\">zde<\/a>.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-be0af349-8cc4-4a10-916c-28f87a4b1f8a\"><h2>Bioinformatick\u00e9 n\u00e1stroje<\/h2>\n<p><strong>ENA (European&nbsp;Nucleotide&nbsp;Archive<\/strong><strong>)<\/strong><a href=\"https:\/\/www.ebi.ac.uk\/ena\/browser\/sequence-search\" target=\"_blank\" rel=\"noreferrer noopener\">&nbsp;https:\/\/www.ebi.ac.uk\/ena\/browser\/sequence-search<\/a><\/p>\n\n\n\n<p>Datab\u00e1ze poskytuj\u00edc\u00ed vy\u010derp\u00e1vaj\u00edc\u00ed z\u00e1znam nukleotidov\u00fdch sekvenc\u00ed z cel\u00e9ho sv\u011bta. Pokr\u00fdv\u00e1 prvotn\u00ed sekvena\u010dn\u00ed data, jejich slo\u017een\u00ed do del\u0161\u00edch \u00fasek\u016f i funk\u010dn\u00ed anotaci. ENA byla vytvo\u0159ena z n\u011bkolika d\u00edl\u010d\u00edch datab\u00e1z\u00ed jako jsou EMBL-Bank, Sequence Read Archive (SRA) a Trace Archive.<\/p>\n\n\n\n<p><strong>MUSCLE (Multiple&nbsp;Sequence&nbsp;Comparison by&nbsp;Log-Expectation)&nbsp;<\/strong><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/msa\/muscle\/\" target=\"_blank\" rel=\"noreferrer noopener\">http:\/\/www.ebi.ac.uk\/Tools\/msa\/muscle\/<\/a><\/p>\n\n\n\n<p>N\u00e1stroj slou\u017e\u00edc\u00ed k mnoho\u010detn\u00e9mu p\u0159i\u0159azen\u00ed (alignment) a porovn\u00e1n\u00ed sekvenc\u00ed, obzvl\u00e1\u0161t\u011b vhodn\u00fd pro aminokyselinov\u00e9 sekvence.<\/p>\n\n\n\n<p><strong>EMBOSS Transeq (European Molecular Biology Open Software Suite Transeq)<\/strong>&nbsp;<a href=\"http:\/\/www.ebi.ac.uk\/Tools\/st\/emboss_transeq\/\" target=\"_blank\" rel=\"noreferrer noopener\">http:\/\/www.ebi.ac.uk\/Tools\/st\/emboss_transeq\/<\/a><\/p>\n\n\n\n<p>N\u00e1stroj, pomoc\u00ed n\u011bho\u017e m\u016f\u017eete p\u0159elo\u017eit nukleotidovou sekvenci do odpov\u00eddaj\u00edc\u00ed proteinov\u00e9 sekvence.<\/p>\n\n\n\n<p><strong>Protein Data Bank in Europe (PDBe)<\/strong>&nbsp;<a rel=\"noreferrer noopener\" href=\"http:\/\/www.ebi.ac.uk\/pdbe\/\" target=\"_blank\">http:\/\/www.ebi.ac.uk\/pdbe\/<\/a><\/p>\n\n\n\n<p>Datab\u00e1ze obsahuj\u00edc\u00ed informace o struktu\u0159e biologick\u00fdch makromolekul.<\/p>\n\n\n\n<p><\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-5498d92f-f4cd-41e3-94ef-bfd891b4e6a4\"><h2>Navigace aktivity<\/h2>\n<p>N\u00ed\u017ee uveden\u00e9 naviga\u010dn\u00ed menu obsahuje jednotliv\u00e9 kroky prvn\u00ed \u00falohy. Za\u010dn\u011bte va\u0161i \u201chonbu za pokladem\u201d kliknut\u00edm na \u201cHonba za pokladem \u2013 GFP \u2013 \u00favod\u201d.<\/p>\n\n\n\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\"><strong>Honba za pokladem &#8211; GFP &#8211; \u00favod<\/strong><\/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><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><\/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","protected":false},"excerpt":{"rendered":"<p>\u2018Treasure hunt\u2019-style introduction to bioinformatics approaches using the protein GFP.<\/p>\n","protected":false},"featured_media":28285,"parent":0,"menu_order":4,"template":"","class_list":["post-28284","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry","age-group-16-19","topic-area-bioinformatics"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28284","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"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/28285"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=28284"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}