{"id":19409,"date":"2015-10-05T19:36:46","date_gmt":"2015-10-05T17:36:46","guid":{"rendered":"http:\/\/emblog.embl.de\/ells\/?post_type=teachingbase&#038;p=19409"},"modified":"2021-06-17T17:47:58","modified_gmt":"2021-06-17T17:47:58","slug":"step-2-comparison-of-nucleotide-sequences","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-2-comparison-of-nucleotide-sequences\/","title":{"rendered":"Step 2: Comparison of nucleotide sequences"},"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-da0d437d-5f99-4d34-b6fa-c991f58a5130\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-78981bee-9962-4382-92d1-7136ffb3d4e5\">Your task<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-9c0782e4-2aaa-4390-accc-3ea3048a359c\">MUSCLE<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-d8ee530d-eb3f-41b4-9c68-04224aba4a8f\">Sequences 1-4<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-9dfee51b-0a31-47d0-a3de-4ab80431fd4d\">Questions<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-c65f4728-e341-4de9-af06-7c0c71a681fe\">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-da0d437d-5f99-4d34-b6fa-c991f58a5130\"><h2>Overview<\/h2>\n<p>A simultaneous comparison of all your nucleotide sequences can be achieved by using the server-based software EMBL-EBI MUSCLE (<span style=\"text-decoration: underline;\">Mu<\/span>ltiple <span style=\"text-decoration: underline;\">S<\/span>equence <span style=\"text-decoration: underline;\">C<\/span>omparison by <span style=\"text-decoration: underline;\">L<\/span>og-<span style=\"text-decoration: underline;\">E<\/span>xpectation). MUSCLE produces so-called <strong>sequence <\/strong><strong>alignments<\/strong>. These alignments can be used to visualise and interpret the relationships between sequences \u2013 and sometimes even between species.<\/p>\n\n\n\n<p>After completing this exercise you should have produced a multiple sequence alignment (on nucleotide level) and will be able to assess roughly which nucleotide sequences are most similar to each other. The nucleotide sequences (input) are provided in the tab &#8220;Sequences&#8221;.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-78981bee-9962-4382-92d1-7136ffb3d4e5\"><h2>Your task<\/h2>\n<p><strong>Proceed as described below:<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>Copy all of the nucleotide sequences which are provided under the tab \u201cSequences\u201d at once (i.e. select and copy the whole block of sequences) (shortcut Ctrl. + C).<\/li><li>Paste the nucleotide sequences into the MUSCLE search box (shortcut Ctrl. + V).<\/li><li>Follow the instructions in the tab \u201cMUSCLE\u201d to align your sequences.<\/li><li>Have a look at the alignment and try to answer the questions in the \u201cQuestions\u201d tab.<\/li><\/ol>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-9c0782e4-2aaa-4390-accc-3ea3048a359c\"><h2>MUSCLE<\/h2>\n<ol class=\"wp-block-list\"><li>Copy all of the nucleotide sequences which are provided under the tab \u201cSequences\u201d at once (i.e. select and copy the whole block of sequences) (shortcut Ctrl. + C).<\/li><li>Paste the nucleotide sequences into the MUSCLE search box (shortcut Ctrl. + V).<\/li><li>In the \u201cSTEP 2\u201d section ensure that \u201c<strong>Output Format<\/strong>\u201d is set at&nbsp;<strong>\u201cClustalW\u201d<\/strong>.<\/li><li>Just click on the large&nbsp;<strong>\u201cSubmit<\/strong>\u201d button and your alignment will be processed.<\/li><li>You will see the results after a few seconds. Have a look at the alignment and try to answer the questions in the \u201cQuestions\u201d tab.<\/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\/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-d8ee530d-eb3f-41b4-9c68-04224aba4a8f\"><h2>Sequences 1-4<\/h2>\n<details  class=\"vf-details\" id=\"\"  >\n<summary class=\"vf-details--summary\">\nSequence 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\">\nSequence 2<\/summary>\n<div class=\"acf-innerblocks-container\">\n\n<pre class=\"wp-block-preformatted\"> <span style=\"word-break:break-all\"<\/span>&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\">\nSequence 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\">\nSequence 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-9dfee51b-0a31-47d0-a3de-4ab80431fd4d\"><h2>Questions<\/h2>\n<p>Have a look at the alignment and try to answer the following questions:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>How do you know whether the nucleotides in the individual sequences are the same or not compared to the other aligned sequences?<\/li><li>Do you think there many corresponding nucleotides? Would you have expected something else?<\/li><li>Which of the two sequences would you judge as being most similar?<\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-c65f4728-e341-4de9-af06-7c0c71a681fe\"><h2>Activity navigation<\/h2>\n<p><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/\">GFP treasure hunt<\/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\/\">GFP treasure hunt introduction<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-1-database-search\/\">Step 1: Database search<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-2-comparison-of-nucleotide-sequences\/\">Step 2: Comparison of nucleotide sequences<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-3-translation-of-mrnas\/\"><strong>Step 3: Translation of mRNAs<\/strong><\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-4-comparison-of-amino-acid-sequences\/\">Step 4: Comparison of amino acid sequences<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/gfp-treasure-hunt\/step-5-structure-of-gfp\/\">Step 5: Structure of GFP<\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":944,"parent":5012,"menu_order":4,"template":"","class_list":["post-19409","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/19409","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\/5012"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/944"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=19409"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}