{"id":36087,"date":"2023-07-06T07:43:02","date_gmt":"2023-07-06T07:43:02","guid":{"rendered":"https:\/\/www.embl.org\/ells\/?post_type=teachingbase&#038;p=36087"},"modified":"2023-07-14T07:16:09","modified_gmt":"2023-07-14T07:16:09","slug":"the-mysterious-protein-a-bioinformatics-expedition","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/","title":{"rendered":"The Mysterious Protein: A Bioinformatics Expedition\u00a0"},"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-e0945ecb-2e21-4f4f-a453-a5318f1c1c86\" data-vf-js-location-nearest-activation-target=\"\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-a513b31d-e1e4-4c5d-a400-7c34f5d3d918\" data-vf-js-location-nearest-activation-target=\"\">Your task<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-597eb4a0-c9b0-4748-9357-7246221dad3e\" data-vf-js-location-nearest-activation-target=\"\">Bioinformatics tools<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-fa3a90a3-2ec9-497d-af2d-1be379559913\" data-vf-js-location-nearest-activation-target=\"\">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-e0945ecb-2e21-4f4f-a453-a5318f1c1c86\"><h2>Overview<\/h2>\n<p>We will dive into the fascinating world of <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">bioinformatics<\/a> to unravel the secrets of <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">proteins<\/a>, one of the fundamental building blocks of molecular biology. Through a series of interactive exercises, we will investigate how proteins are made, how they look and how they have evolved across species. Join us on this fictional scientific adventure that is intertwined with real-life research activities at EMBL, and gain insights into cutting-edge research methodologies.<\/p>\n\n\n\n<p>The aim of this activity is to deepen our understanding of proteins and their <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">evolution<\/a>, while also providing valuable insights into the practical applications of bioinformatics in scientific research.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-a513b31d-e1e4-4c5d-a400-7c34f5d3d918\"><h2>Your task<\/h2>\n<p>During the <a rel=\"noreferrer noopener\" href=\"https:\/\/www.embl.org\/about\/info\/trec\/\" target=\"_blank\">TREC<\/a> (Traversing European Coastlines) expedition, researchers gather a wide array of biological samples from the European coastline to investigate the coastal ecosystems. These samples are obtained from soil, sediments, aerosol, shallow water and sea, and are meticulously analysed using scientific techniques such as microscopy or\u00a0<a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">DNA sequencing<\/a>.\u00a0<\/p>\n\n\n\n<p>Recently, the researchers stumbled upon a perplexing discovery within one of their samples from the shallow water \u2014 an unidentified DNA sequence that does not match any known sequence. Intrigued by this finding, the TREC researchers have a challenge for you: Can you help them to identify the protein encoded by this sequence and decipher its biological function? Furthermore, can you assist in identifying the species of origin and exploring its evolutionary relationships with other organisms?<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-597eb4a0-c9b0-4748-9357-7246221dad3e\"><h2>Bioinformatics tools<\/h2>\n<p>Most of the tools we will employ during this activity have been developed and made<strong> freely <\/strong>available to scientists all over the world by EMBL-EBI.<\/p>\n\n\n\n<p><strong>EMBOSS Transeq<br><\/strong>Link: <a rel=\"noreferrer noopener\" href=\"https:\/\/www.ebi.ac.uk\/Tools\/st\/emboss_transeq\/\" target=\"_blank\">https:\/\/www.ebi.ac.uk\/Tools\/st\/emboss_transeq\/<\/a><br>A tool used to translate nucleic acid sequences (<a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">DNA<\/a> or <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">RNA<\/a>) into their corresponding amino acid sequences.<\/p>\n\n\n\n<p><strong>NCBI BLAST+ (Basic Local Alignment Search Tool)<\/strong><br>Link: <a href=\"http:\/\/www.ebi.ac.uk\/Tools\/sss\/ncbiblast\/\" target=\"_blank\" rel=\"noreferrer noopener\">http:\/\/www.ebi.ac.uk\/Tools\/sss\/ncbiblast\/<br><\/a>A tool used to identify and compare biological sequence information, such as amino acid sequences. It enables researchers to compare a subject protein (referred to as a query) with a database of sequences, making it useful in identifying unknown proteins.&nbsp;<\/p>\n\n\n\n<p><strong>Clustal Omega<\/strong>&nbsp;<br>Link: <a href=\"https:\/\/www.ebi.ac.uk\/Tools\/msa\/clustalo\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/www.ebi.ac.uk\/Tools\/msa\/clustalo\/<\/a><br>A tool designed for aligning and comparing multiple sequences, specifically suited for amino acid sequences.&nbsp;<\/p>\n\n\n\n<p><strong>Simple Phylogeny<br><\/strong>Link: <a rel=\"noreferrer noopener\" href=\"https:\/\/www.ebi.ac.uk\/Tools\/phylogeny\/simple_phylogeny\/\" target=\"_blank\">https:\/\/www.ebi.ac.uk\/Tools\/phylogeny\/simple_phylogeny\/<\/a><br>A tool designed to perform basic <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">phylogenetic<\/a> analysis on a multiple sequence alignment.<\/p>\n\n\n\n<p><strong>UniProt (Universal Protein Resource) database<br><\/strong>Link: <a href=\"http:\/\/www.uniprot.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">http:\/\/www.uniprot.org\/<br><\/a>A comprehensive catalogue of protein information, including protein sequences and their functions.<\/p>\n\n\n\n<p><strong>AlphaFold Database<br><\/strong>Link: <a rel=\"noreferrer noopener\" href=\"https:\/\/alphafold.ebi.ac.uk\/\" target=\"_blank\">https:\/\/alphafold.ebi.ac.uk\/<\/a>\u00a0<br>A database for protein structure predictions. AlphaFold is an <a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/ells-glossary\/\" target=\"_blank\" rel=\"noreferrer noopener\">artificial intelligence (AI)<\/a> system that can predict a protein\u2019s 3D structure based on its amino acid sequence. The AlphaFold Database is also integrated into UniProt.<\/p>\n\n\n\n<p><strong>Note:<\/strong> These tools require some time for the calculations. Therefore, a little patience may be necessary.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-fa3a90a3-2ec9-497d-af2d-1be379559913\"><h2>Activity navigation<\/h2>\n<ul class=\"wp-block-list\">\n<li><strong><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/the-mysterious-protein-a-bioinformatics-expedition\/\" target=\"_blank\" rel=\"noreferrer noopener\">Introductory page<\/a><\/strong><\/li>\n\n\n\n<li><a href=\"http:\/\/embl.org\/ells\/teachingbase\/part-1-from-dna-to-protein-sequence\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 1: From DNA to protein sequence<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-2-protein-identity-and-function\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-2-protein-identity-and-function\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 2: Protein identity and function<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-3-multiple-sequence-alignment\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 3: Multiple sequence alignment&nbsp;<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-4-phylogenetic-analysis\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-4-phylogenetic-analysis\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 4: Phylogenetic analysis&nbsp;<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-5-structural-analysis\/\" data-type=\"URL\" data-id=\"https:\/\/www.embl.org\/ells\/teachingbase\/part-5-structural-analysis\/\" target=\"_blank\" rel=\"noreferrer noopener\">Part 5: Structural analysis<\/a><\/li>\n<\/ul>\n<\/section>\n<\/div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>A bioinformatics resource to teach protein structure and species evolution<\/p>\n","protected":false},"featured_media":36261,"parent":0,"menu_order":0,"template":"","class_list":["post-36087","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry","age-group-16-19","topic-area-biochemistry","topic-area-bioinformatics","topic-area-evolutionary-biology","topic-area-structural-computational-biology"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/36087","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\/36261"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=36087"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}