{"id":28440,"date":"2015-10-05T13:45:15","date_gmt":"2015-10-05T11:45:15","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-1-search-for-protein-identity\/"},"modified":"2021-06-18T15:00:15","modified_gmt":"2021-06-18T15:00:15","slug":"part-1-search-for-protein-identity","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-1-search-for-protein-identity\/?lang=cs","title":{"rendered":"\u010c\u00e1st 1: Hled\u00e1n\u00ed identity nezn\u00e1m\u00e9ho proteinu"},"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-4e25ab7e-2c41-42d5-aa00-09c96f8b4be9\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-8a3cf4ad-9803-439b-a042-f9ca447e4ee6\">Va\u0161e \u00faloha<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-439c3d0e-3b26-4d30-beea-ef424ad8d3c3\">Sekvence<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-a6dc31f5-7afe-43cb-9e43-f2728ace9ae5\">Protein BLAST<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-7a5ab492-eb0a-4cd9-9b74-10d11126f360\">Ot\u00e1zky k \u00faloze<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-36f3994d-b165-4987-a6b7-5098d466eec3\">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-4e25ab7e-2c41-42d5-aa00-09c96f8b4be9\"><h2>Overview<\/h2>\n<p>Pr\u00e1v\u011b se n\u00e1m poda\u0159ilo vyklonovat nov\u00fd gen a dnes jsme kone\u010dn\u011b z\u00edskali v\u00fdsledky sekvena\u010dn\u00ed reakce. Poda\u0159ilo se n\u00e1m p\u0159elo\u017eit DNA sekvenci do proteinov\u00e9, bohu\u017eel v\u0161ak nev\u00edme nic o funkci tohoto genu. Proto se pokus\u00edme v internetov\u00e9 bioinformatick\u00e9 datab\u00e1zi, kter\u00e1 ji\u017e obsahuje mnoho zn\u00e1m\u00fdch protein\u016f, naj\u00edt velmi podobn\u00e9 sekvence a zjistit, jestli se n\u00e1\u0161 protein n\u00e1padn\u011b nepodob\u00e1 n\u011bkter\u00e9mu proteinu, jeho\u017e biologick\u00e1 funkce je ji\u017e zn\u00e1ma.<\/p>\n\n\n\n<p>P\u0159i vypracov\u00e1v\u00e1n\u00ed \u00falohy pros\u00edm sledujte pokyny v z\u00e1lo\u017ece \u201cVa\u0161e \u00faloha\u201d a pokuste se odpov\u011bd\u011bt na ot\u00e1zky ke ka\u017ed\u00e9mu cvi\u010den\u00ed.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-8a3cf4ad-9803-439b-a042-f9ca447e4ee6\"><h2>Va\u0161e \u00faloha<\/h2>\n<p><strong>Postupujte n\u00e1sledovn\u011b:<\/strong><\/p>\n\n\n\n<p><strong>1.<\/strong> Z\u00e1lo\u017eka \u201cSekvence\u201d obsahuje aminokyselinovou sekvenci na\u0161eho nov\u011b vyklonovan\u00e9ho nezn\u00e1m\u00e9ho proteinu \u201cBovine_Protein\u201d. (tedy alespo\u0148 v\u00edme, \u017ee jsme gen vyklonovali z b\u00fdka).<br><strong>2.<\/strong> Zkop\u00edrujte sekvenci do pam\u011bti po\u010d\u00edta\u010de a pokra\u010dujte z\u00e1lo\u017ekou \u201cProtein BLAST\u201d.<br><strong>3.<\/strong> \u0158i\u010fte se pokyny v z\u00e1lo\u017ece \u201cProtein BLAST\u201d a pokuste se odpov\u011bd\u011bt na ot\u00e1zky v z\u00e1lo\u017ece \u201cOt\u00e1zky\u201d.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-439c3d0e-3b26-4d30-beea-ef424ad8d3c3\"><h2>Sekvence<\/h2>\n<p>A\u0161e vstupn\u00ed sekvence (&#8220;nezn\u00e1m\u00fd&#8221; protein):<\/p>\n\n\n\n<pre class=\"wp-block-code vf-u-text--break\"><code>Bovine_Protein\nMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA<\/code><\/pre>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-a6dc31f5-7afe-43cb-9e43-f2728ace9ae5\"><h2>Protein BLAST<\/h2>\n<p><strong><strong>1.<\/strong> <\/strong>Pou\u017eijte n\u00ed\u017ee zobrazen\u00fd n\u00e1stroj Protein BLAST (Basic Local Alignment Search Tool).<strong><br><strong>2. <\/strong><\/strong>Zkop\u00edrujte a vlo\u017ete va\u0161\u00ed aminokyselinovou sekvenci (v\u010detn\u011b znam\u00e9nka &#8220;&gt;&#8221;) do okna &#8220;Query&#8221;. Pot\u00e9 m\u016f\u017eete vlo\u017eit kr\u00e1tk\u00fd popis (nap\u0159. &#8220;nezn\u00e1m\u00fd protein&#8221;). Zkontrolujte, jestli je v pol\u00ed\u010dku &#8220;Parameters&#8221; zatr\u017eena mo\u017enost &#8220;blastp&#8221; a kliknut\u00edm na &#8220;Submit&#8221; ode\u0161lete v\u00e1\u0161 &#8220;job&#8221; ke zpracov\u00e1n\u00ed na serveru.<strong><br><strong>3.<\/strong> <\/strong>Jakmile obdr\u017e\u00edte v\u00fdsledky, projd\u011bte je a pokuste se zodpov\u011bd\u011bt na Ot\u00e1zky k \u00faloze.<\/p>\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\/sss\/ncbiblast\/\" 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-7a5ab492-eb0a-4cd9-9b74-10d11126f360\"><h2>Ot\u00e1zky k \u00faloze<\/h2>\n<p><strong><strong>1.<\/strong> <\/strong>Kter\u00fd protein v datab\u00e1zi vykazuje nejlep\u0161\u00ed &#8220;hit&#8221; k va\u0161emu nezn\u00e1m\u00e9mu proteinu?<strong><br><strong>2.<\/strong> <\/strong>Na kolik procent je tento nejlep\u0161\u00ed hit identick\u00fd va\u0161emu proteinu?<strong><br><strong>3.<\/strong> <\/strong>Jak\u00e1 je biologick\u00e1 funkce tohoto nejpodobn\u011bj\u0161\u00edho proteinu? (V tabulce v\u00fdsledk\u016f klikn\u011bte na odkaz v druh\u00e9m sloupci (DB:ID) a prohl\u00e9dn\u011bte si informace v pol\u00ed\u010dku &#8220;General annotation (Comments)&#8221;.)<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-36f3994d-b165-4987-a6b7-5098d466eec3\"><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><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><\/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\"><strong>Part 2: Multiple sequence alignment of protein sequences<\/strong><\/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":"","protected":false},"featured_media":28441,"parent":28420,"menu_order":4,"template":"","class_list":["post-28440","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28440","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\/28420"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/28441"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=28440"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}