{"id":28420,"date":"2014-01-14T12:36:22","date_gmt":"2014-01-14T11:36:22","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/"},"modified":"2021-06-17T12:48:37","modified_gmt":"2021-06-17T12:48:37","slug":"opsins-bioinformatics","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/?lang=cs","title":{"rendered":"P\u00e1tr\u00e1n\u00ed po evoluci sv\u011btlo\u010divn\u00fdch protein\u016f"},"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-aeffaa3d-a89c-4cec-a954-6a3ae32d7227\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-0d944763-e9ee-4ccc-a55e-ee51613c0e16\">Technick\u00e9 po\u017eadavky<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-aa0a2b85-50ab-4cdf-92c9-9fcd7d705013\">Bioinformatick\u00e9 n\u00e1stroje<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-7e7fdaaf-84b8-49f5-8461-ac9c544770a0\">Activity navigation<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-aeffaa3d-a89c-4cec-a954-6a3ae32d7227\"><h2>Overview<\/h2>\n<p>V t\u00e9to \u00faloze se pokus\u00edme pomoc\u00ed bioinformatick\u00fdch p\u0159\u00edstup\u016f dozv\u011bd\u011bt n\u011bco o molekul\u00e1rn\u00ed evoluci gen\u016f. Nejd\u0159\u00edve pou\u017eijeme BLAST k identifikaci \u201cnezn\u00e1m\u00e9ho\u201d proteinu a n\u00e1sledn\u011b z\u00edsk\u00e1me z bioinformatick\u00fdch datab\u00e1z\u00ed z\u00e1kladn\u00ed infromace o jeho biologick\u00e9 \u00faloze. Abychom nahl\u00e9dli do evoluce t\u00e9to proteinov\u00e9 rodiny, vytvo\u0159\u00edme mnoho\u010detn\u00e1 p\u0159i\u0159azen\u00ed (multiple sequence alignment) homologn\u00edch proteinov\u00fdch sekvenc\u00ed, najdeme konzervovan\u00e9 i variabiln\u00ed \u00faseky, a pokus\u00edme se identifikovat aminokyseliny z\u00e1sadn\u011b d\u016fle\u017eit\u00e9 pro zachov\u00e1n\u00ed biochemick\u00e9 funkce t\u011bchto protein\u016f. V n\u00e1sleduj\u00edc\u00edm cvi\u010den\u00ed se nau\u010d\u00edme, jak m\u016f\u017eeme z proteinov\u00fdch sekvenc\u00ed vytvo\u0159it fylogenetick\u00fd evolu\u010dn\u00ed strom a porozum\u011bt tak pojm\u016fm homolog, paralog a ortholog a prozkoumat tyto vlastnosti v r\u00e1mci na\u0161\u00ed proteinov\u00e9 rodiny. Na z\u00e1v\u011br si je\u0161t\u011b prohl\u00e9dneme 3D prostorovou strukturu vybran\u00e9ho z\u00e1stupce t\u011bchto protein\u016f.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-0d944763-e9ee-4ccc-a55e-ee51613c0e16\"><h2>Technick\u00e9 po\u017eadavky<\/h2>\n<p>Tato \u00faloha byla navr\u017eena a testov\u00e1na pro opera\u010dn\u00ed syst\u00e9my Windows. U\u017eivatel\u00e9 po\u010d\u00edta\u010d\u016f Apple Mac mohou m\u00edt probl\u00e9my s Javou b\u011bhem pou\u017e\u00edv\u00e1n\u00ed JalView a Astex Viewer. Doporu\u010den\u00fd internetov\u00fd prohl\u00ed\u017ee\u010d pro tuto \u00falohu je Mozilla Firefox.<\/p>\n\n\n\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 <a href=\"http:\/\/www.java.com\/en\/\" target=\"_blank\" rel=\"noreferrer noopener\">java.com<\/a>. Informace jak povolit Javu ve va\u0161em prohl\u00ed\u017ee\u010di najdete <a href=\"http:\/\/www.java.com\/en\/\" target=\"_blank\" rel=\"noreferrer noopener\">zde<\/a>.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-aa0a2b85-50ab-4cdf-92c9-9fcd7d705013\"><h2>Bioinformatick\u00e9 n\u00e1stroje<\/h2>\n<h3 class=\"wp-block-heading\"><strong>MUSCLE (Multiple Sequence Comparison by Log-Expectation)<\/strong><\/h3>\n\n\n\n<p><a rel=\"noopener noreferrer\" href=\"http:\/\/www.ebi.ac.uk\/Tools\/msa\/muscle\/\" target=\"_blank\">http:\/\/www.ebi.ac.uk\/Tools\/msa\/muscle\/<\/a><br>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<h3 class=\"wp-block-heading\"><strong>Protein BLAST (Basic Local Alignment Search Tool)<\/strong><\/h3>\n\n\n\n<p><a rel=\"noopener noreferrer\" href=\"http:\/\/www.ebi.ac.uk\/Tools\/sss\/ncbiblast\/\" target=\"_blank\">http:\/\/www.ebi.ac.uk\/Tools\/sss\/ncbiblast\/<\/a><br>N\u00e1stroj prohled\u00e1vaj\u00edc\u00ed proteinov\u00e9 datab\u00e1ze na z\u00e1klad\u011b proteinov\u00e9 sekvence. Vyhled\u00e1v\u00e1 a porovn\u00e1v\u00e1 podobn\u00e9 \u00faseky mezi dv\u011bma proteinov\u00fdmi sekvencemi a m\u016f\u017ee tak b\u00fdt pou\u017eit\u00fd k nalezen\u00ed identity nezn\u00e1m\u00fdch proteinov\u00fdch sekvenc\u00ed.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>Uniprot<\/strong><\/h3>\n\n\n\n<p><a rel=\"noopener noreferrer\" href=\"http:\/\/www.uniprot.org\/\" target=\"_blank\">http:\/\/www.uniprot.org\/<\/a><br>Katalog informac\u00ed o proteinech v\u010detn\u011b sekvenc\u00ed a biologick\u00fdch funkc\u00ed.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>Protein Data Bank in Europe (PDBe)&nbsp;<\/strong><\/h3>\n\n\n\n<p><a rel=\"noopener noreferrer\" href=\"http:\/\/www.ebi.ac.uk\/pdbe\/\" target=\"_blank\">http:\/\/www.ebi.ac.uk\/pdbe\/<\/a><br>Datab\u00e1ze obsahuj\u00edc\u00ed informace o struktu\u0159e biologick\u00fdch makromolekul.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>Glossary<\/strong><\/h3>\n\n\n\n<p>Check out the <a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\">ELLS Glossary<\/a> for a growing number of bioinformatics-related terms (in English).<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-7e7fdaaf-84b8-49f5-8461-ac9c544770a0\"><h2>Activity navigation<\/h2>\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28420\">P\u00e1tr\u00e1n\u00ed po evoluci sv\u011btlo\u010divn\u00fdch protein\u016f<\/a><\/li><li><strong><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-1-search-for-protein-identity\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28440\">\u010c\u00e1st 1: Hled\u00e1n\u00ed identity nezn\u00e1m\u00e9ho proteinu<\/a><\/strong><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28454\">Part 2: Multiple sequence alignment of protein sequences<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-3-phylogenetic-analysis-of-aligned-protein-sequences\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28474\">\u010c\u00e1st 3: Fylogenetick\u00e1 anal\u00fdza proteinov\u00fdch sekvenc\u00ed<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-4-topological-and-structural-analysis-of-proteins\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28497\">\u010c\u00e1st 4: Topologick\u00e1 a strukturn\u00ed anal\u00fdza protein\u016f<\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>Uses bioinformatics to explore the evolution of light-sensitive proteins.<\/p>\n","protected":false},"featured_media":28400,"parent":0,"menu_order":5,"template":"","class_list":["post-28420","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry","age-group-16-19","topic-area-evolutionary-biology"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28420","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\/28400"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=28420"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}