{"id":28474,"date":"2015-10-05T13:46:40","date_gmt":"2015-10-05T11:46:40","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-3-phylogenetic-analysis-of-aligned-protein-sequences\/"},"modified":"2021-06-16T14:40:33","modified_gmt":"2021-06-16T14:40:33","slug":"part-3-phylogenetic-analysis-of-aligned-protein-sequences","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-3-phylogenetic-analysis-of-aligned-protein-sequences\/?lang=cs","title":{"rendered":"\u010c\u00e1st 3: Fylogenetick\u00e1 anal\u00fdza proteinov\u00fdch sekvenc\u00ed"},"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-3687f4f2-ec44-4a8b-b9d9-892ccf767415\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-021ae0ac-4eb7-45e0-a5a3-34b30f9bad18\">Va\u0161e \u00faloha<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-adf6fadf-79f2-42ed-a503-272a803893c1\">MUSCLE<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-c6293ee4-0b5e-40e0-a9c1-6cc5cf1cd33e\">Ot\u00e1zky<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-62917c2a-aa30-4312-ad3c-464533410cc0\">Dopl\u0148kov\u00e9 cvi\u010den\u00ed<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-90482065-e743-4d9f-8b75-fb7b30a95db5\">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-3687f4f2-ec44-4a8b-b9d9-892ccf767415\"><h2>Overview<\/h2>\n<p>V t\u00e9to \u010d\u00e1sti \u00falohy se nau\u010d\u00edme vytvo\u0159it fylogenetick\u00fd strom na\u0161ich 24 proteinov\u00fdch sekvenc\u00ed. K tomu v\u0161ak nejprve mus\u00edme odstranit nekonzervovan\u00e9 (p\u0159\u00edtomn\u00e9 ne ve v\u0161ech proteinech) aminokyselinov\u00e9 zbytky, kter\u00e9 jsme identifikovali v mnoho\u010detn\u00e9m p\u0159i\u0159azen\u00ed v \u010d\u00e1sti 2 na\u0161\u00ed \u00falohy.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-021ae0ac-4eb7-45e0-a5a3-34b30f9bad18\"><h2>Va\u0161e \u00faloha<\/h2>\n<p><strong>\u0158i\u010fte se n\u00e1sleduj\u00edc\u00edmi pokyny:<\/strong><\/p>\n\n\n\n<p><strong>1. <\/strong>Upravte mnoho\u010detn\u00e9 p\u0159i\u0159azen\u00ed, kter\u00e9 jste z\u00edskali v \u010d\u00e1sti 2 a odstra\u0148te nekonzervovan\u00e9 aminokyselinov\u00e9 zbytky.<\/p>\n\n\n\n<p><strong>i.<\/strong> Vra\u0165te se do okna JalView s mnoho\u010detn\u00fdm p\u0159i\u0159azen\u00edm (v\u00fdsledkek \u010d\u00e1sti 2).<\/p>\n\n\n\n<p><strong>ii.<\/strong> V JalView sma\u017ete v\u0161echny jednotliv\u00e9 pozice a \u00faseky sekvenc\u00ed, kter\u00e9 nejsou vysoce konzervovan\u00e9, tj. nejsou p\u0159\u00edtomny v ostatn\u00edch sekvenc\u00edch: Naje\u010fte kurzorem my\u0161i nad prvn\u00ed \u0159\u00e1dek cel\u00e9ho alignmentu a pomoc\u00ed lev\u00e9ho kliku a ta\u017een\u00edm my\u0161i doprava nebo doleva vyberte sloupce (objev\u00ed se \u010derven\u00e9 or\u00e1mov\u00e1n\u00ed), nyn\u00ed stiskn\u011bte na kl\u00e1vesnici tla\u010d\u00edtko backspace.<\/p>\n\n\n\n<p><strong>iii.<\/strong> Po editov\u00e1n\u00ed ulo\u017ete alignment jako FASTA soubor: File &gt; Output to Textbox &gt; FASTA. Vytvo\u0159te nov\u00fd textov\u00fd dokument kliknut\u00edm prav\u00e9ho tla\u010d\u00edtka my\u0161i na plochu va\u0161eho po\u010d\u00edta\u010de: New &gt; Text Document. Zkop\u00edrujte a vlo\u017ete ulo\u017een\u00fd alignment do tohoto nov\u00e9ho souboru a nechte jej otev\u0159en\u00fd pro pozd\u011bj\u0161\u00ed pou\u017eit\u00ed.<\/p>\n\n\n\n<p><strong>Pozn\u00e1mka:<\/strong> jestli se v\u00e1m z jak\u00e9hokoliv d\u016fvodu mnoho\u010detn\u00e9 p\u0159i\u0159azen\u00ed nepoda\u0159ilo upravit a ulo\u017eit, v tuto chv\u00edli a pro \u00fa\u010dely tohoto cvi\u010den\u00ed to nevad\u00ed. Sekvence byly toti\u017e vybr\u00e1ny tak, \u017ee poskytuj\u00ed slu\u0161n\u00fd fylogenetick\u00fd strom i bez rozs\u00e1hl\u00e9 editace. Av\u0161ak nezapome\u0148te, \u017ee v re\u00e1ln\u00e9 situaci mus\u00edte v\u017edy odstranit nep\u0159i\u0159aditeln\u00e9 \u00faseky p\u0159edt\u00edm ne\u017e se pokus\u00edte sestrojit fylogenetick\u00fd strom, jinak nem\u00e1 strom \u017e\u00e1dnou vypov\u00eddac\u00ed hodnotu a m\u016f\u017ee v\u00e9st k velice chybn\u00fdm z\u00e1v\u011br\u016fm!<\/p>\n\n\n\n<p><strong>2.<\/strong> Vlo\u017ete editovan\u00fd alignment do vstupn\u00edho pol\u00ed\u010dka programu MUSCLE (v z\u00e1lo\u017ece MUSCLE) a jako v\u00fdstupn\u00ed form\u00e1t zvolte &#8220;ClustalW&#8221; (output format &#8220;ClustalW&#8221;). D\u00e1le se \u0159i\u010fte pokyny v z\u00e1lo\u017ece &#8220;MUSCLE&#8221;.<\/p>\n\n\n\n<p><strong>3.<\/strong> Pokuste se odpov\u011bd\u011bt na ot\u00e1zky.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-adf6fadf-79f2-42ed-a503-272a803893c1\"><h2>MUSCLE<\/h2>\n<p><strong>1.<\/strong> Vlo\u017ete editovan\u00fd alignment do vstupn\u00edho pol\u00ed\u010dka programu MUSCLE (v z\u00e1lo\u017ece MUSCLE) a jako v\u00fdstupn\u00ed form\u00e1t zvolte &#8220;ClustalW&#8221; (output format &#8220;ClustalW&#8221;).<\/p>\n\n\n\n<p><strong>2. <\/strong>Pot\u00e9, co obdr\u017e\u00edte v\u00fdsledkovou str\u00e1nku, klikn\u011bte na &#8220;Send to ClustalW_Phylogeny&#8221; a pozd\u011bji na str\u00e1nce ClustalW phylogeny &#8211; Step 2 vyberte n\u00e1sleduj\u00edc\u00ed:<br>&#8220;Tree format&#8221;: Default; &#8220;Distance correction&#8221;: ON; &#8220;Exclude gaps&#8221;: ON (Toto je nejd\u016fle\u017eit\u011bj\u0161\u00ed krok. Jestli\u017ee jste ji\u017e sekvence editovali v JalView, asi jste u\u017e odstranili v\u0161echny pozice, ve kter\u00fdch se alespo\u0148 v jedn\u00e9 sekvenci vyskytuje mezera. Za\u0161krtnut\u00edm t\u00e9to mo\u017enosti nicm\u00e9n\u011b zaru\u010duje, \u017ee i opomenut\u00e9 mezery budou pomoc\u00ed algoritmu odstran\u011bny.) &#8220;Clustering method&#8221;: UPGMA; &#8220;P.I.M.&#8221;: ON<\/p>\n\n\n\n<p><strong>3.<\/strong> Klikn\u011bte na tla\u010d\u00edtko &#8220;Submit&#8221;.<\/p>\n\n\n\n<p><strong>4.<\/strong> V okn\u011b s v\u00fdsledky najdete pod n\u00e1zvem &#8220;Phylogram&#8221; diagram va\u0161eho fylogenetick\u00e9ho stromu. M\u016f\u017eete vyzkou\u0161et vybrat &#8220;Branch length&#8221; jako &#8220;Real&#8221;, \u010d\u00edm\u017e se v\u00e1m zobraz\u00ed d\u00e9lky v\u011btv\u00ed odr\u00e1\u017eej\u00edc\u00edch evolu\u010dn\u00ed vzd\u00e1lenost sekvenc\u00ed. Pro dal\u0161\u00ed \u010d\u00e1st cvi\u010den\u00ed je v\u0161ak vhodn\u011bj\u0161\u00ed zobrazen\u00ed jako &#8220;Cladogram&#8221;. Pozorn\u011b si prohl\u00e9dn\u011bte strukturu stromu 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\/msa\/muscle\/\" 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-c6293ee4-0b5e-40e0-a9c1-6cc5cf1cd33e\"><h2>Ot\u00e1zky<\/h2>\n<p><strong>1.<\/strong> Prohl\u00e9dn\u011bte si strukturu stromu. M\u011bli byste vid\u011bt jednu sekvenci, kter\u00e1 le\u017e\u00ed &#8220;vn\u011b&#8221; stromu a tvo\u0159\u00ed tak tzv. &#8220;outgroup&#8221; ke v\u0161em ostatn\u00edm. Kter\u00e1 z nich to je? Pro\u010d mysl\u00edte, \u017ee je to pr\u00e1v\u011b tato sekvence?<br><strong>2.<\/strong> Zbytek stromu je rozd\u011blen na dv\u011b hlavn\u00ed skupiny. Odr\u00e1\u017e\u00ed toto rozd\u011blen\u00ed evolu\u010dn\u00ed vztahy mezi \u017eivo\u010di\u0161n\u00fdmi druhy, ze kter\u00fdch tyto sekvence poch\u00e1z\u00ed? Jsou zde n\u011bjak\u00e9 v\u00fdjimky?<\/p>\n\n\n\n<p>Podrobn\u011bj\u0161\u00ed anal\u00fdzu evoluce opsin\u016f m\u016f\u017eete prov\u00e9st v kr\u00e1tk\u00e9m dopl\u0148kov\u00e9m cvi\u010den\u00ed (z\u00e1lo\u017eka Dopl\u0148kov\u00e9 cvi\u010den\u00ed) nebo rovnou pokra\u010dov\u00e1t \u010dtvrtou \u010d\u00e1st\u00ed kliknut\u00edm na n\u00ed\u017ee uveden\u00fd odkaz.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-62917c2a-aa30-4312-ad3c-464533410cc0\"><h2>Dopl\u0148kov\u00e9 cvi\u010den\u00ed<\/h2>\n<h3 class=\"wp-block-heading\"><strong>Podrobn\u011bj\u0161\u00ed anal\u00fdza mnoho\u010detn\u00e9ho p\u0159i\u0159azen\u00ed<\/strong><\/h3>\n\n\n\n<p>\u00dasp\u011b\u0161n\u011b jste vytvo\u0159ili fylogenetick\u00fd strom opsinov\u00fdch protein\u016f. V tomto kr\u00e1tk\u00e9m cvi\u010den\u00ed pou\u017eijeme znovu jejich sekven\u010dn\u00ed alignment, abychom v\u00edce porozum\u011bli jejich evoluci.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>Va\u0161e \u00faloha<\/strong><\/h3>\n\n\n\n<p>Vra\u0165te se zp\u011bt do okna JalView a pokuste se se\u0159adit sekvence do dvou skupin od shora dol\u016f tak, jak jsou se\u0159azeny ve fylogenetick\u00e9m stromu (&#8220;Cladogram&#8221; view). Sekven\u010dn\u00ed \u0159\u00e1dky m\u016f\u017eete voln\u011b posouvat kliknut\u00edm na n\u00e1zev sekvence a n\u00e1sledn\u00fdm stisknut\u00edm \u0161ipky nahoru\/dol\u016f. Ignorujte sekvenci &#8220;Danio_mel_rec1A&#8221; (vyma\u017ete ji kliknut\u00edm na jej\u00ed n\u00e1zev a n\u00e1sledn\u00fdm stisknut\u00edm kl\u00e1vesy backspace, p\u0159\u00edpadn\u011b ji p\u0159esu\u0148te \u00fapln\u011b nahoru \u010di dol\u016f).<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>Ot\u00e1zky<\/strong><\/h3>\n\n\n\n<p><strong>1. <\/strong>Receptory sp\u0159a\u017een\u00e9 s G-proteiny (G protein-coupled receptors, GPCRs) obsahuj\u00ed na konci sedm\u00e9 (posledn\u00ed) transmembr\u00e1nov\u00e9 dom\u00e9ny tripeptidov\u00fd motiv, kter\u00fd je zapot\u0159eb\u00ed k vazb\u011b G-alfa proteinu. Najdete takov\u00fd tripeptid na rozhran\u00ed sedm\u00e9 transmembr\u00e1nov\u00e9 dom\u00e9ny a C-koncov\u00e9ho \u00faseku opsinov\u00fdch sekvenc\u00ed. Tyto tripeptidy jsou evolu\u010dn\u011b konzervovan\u00e9 a rovn\u011b\u017e odr\u00e1\u017eej\u00ed seskupov\u00e1n\u00ed opsinov\u00fdch sekvenc\u00ed ve fylogenetick\u00e9m stromu.<br><strong>2.<\/strong> Napad\u00e1 v\u00e1s d\u016fvod, pro\u010d jsou tyto tripeptidy tak evolu\u010dn\u011b konzervovan\u00e9?<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-90482065-e743-4d9f-8b75-fb7b30a95db5\"><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\">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\"><strong>\u010c\u00e1st 4: Topologick\u00e1 a strukturn\u00ed anal\u00fdza protein\u016f<\/strong><\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":28475,"parent":28420,"menu_order":2,"template":"","class_list":["post-28474","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28474","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\/28475"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=28474"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}