{"id":40897,"date":"2023-08-03T14:55:42","date_gmt":"2023-08-03T09:10:42","guid":{"rendered":"https:\/\/microbenotes.com\/nucleotide-sequences-database\/"},"modified":"2023-08-03T14:55:42","modified_gmt":"2023-08-03T09:10:42","slug":"nucleotide-sequences-database","status":"publish","type":"post","link":"https:\/\/microbenotes.com\/nucleotide-sequences-database\/","title":{"rendered":"Nucleotide Databases- Definition, Types, Examples, Uses"},"content":{"rendered":"\n<p><a href=\"https:\/\/microbenotes.com\/biological-databases-types-and-importance\/\" data-type=\"post\" data-id=\"1691\">Biological databases<\/a> store and organize biological data for easy retrieval of information. These centralized resources contain <a href=\"https:\/\/microbenotes.com\/dna-deoxyribonucleic-acid\/\" data-type=\"post\" data-id=\"29063\">DNA<\/a> and protein sequences and their associated information.\u00a0<\/p>\n\n\n\n<p><strong>Nucleotide databases are a type of biological database containing genetic information, which includes DNA and RNA sequences that come from a variety of sources, including whole genomes, transcriptomes, and individual genes.<\/strong><\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" src=\"https:\/\/microbenotes.com\/wp-content\/uploads\/2023\/04\/Nucleotide-Databases.jpg\" alt=\"Nucleotide Databases\" class=\"wp-image-40639\"\/><figcaption class=\"wp-element-caption\">Figure: Nucleotide Databases. Image Sources: Respective database websites.<\/figcaption><\/figure>\n\n\n\n<p>There are several nucleotide databases. Some of the most popular nucleotide databases are:<\/p>\n\n\n\n<p style=\"font-size:28px\"><strong>International Nucleotide Sequence Database Collaboration<\/strong><\/p>\n\n\n\n<p>The International Nucleotide Sequence Database Collaboration (INSDC) is a group of three organizations &#8211; GenBank, EMBL, and DDBJ &#8211; that collect and share nucleotide sequence data.<\/p>\n\n\n\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_65 counter-hierarchy ez-toc-counter ez-toc-custom ez-toc-container-direction\">\n<div class=\"ez-toc-title-container\">\n<p class=\"ez-toc-title \" >Table of Contents<\/p>\n<span class=\"ez-toc-title-toggle\"><a href=\"#\" class=\"ez-toc-pull-right ez-toc-btn ez-toc-btn-xs ez-toc-btn-default ez-toc-toggle\" aria-label=\"Toggle Table of Content\"><span class=\"ez-toc-js-icon-con\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #0a0a0a;color:#0a0a0a\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #0a0a0a;color:#0a0a0a\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/span><\/a><\/span><\/div>\n<nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/#genbank\" title=\"GenBank\">GenBank<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/#european-molecular-biology-laboratory-embl\" title=\"European Molecular Biology Laboratory (EMBL)\">European Molecular Biology Laboratory (EMBL)<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/#dna-data-bank-of-japan-ddbj\" title=\"DNA Data Bank of Japan (DDBJ)\">DNA Data Bank of Japan (DDBJ)<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/#genome-sequence-archive-gsa\" title=\"Genome Sequence Archive (GSA)\">Genome Sequence Archive (GSA)<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/#single-nucleotide-polymorphism-database-dbsnp\" title=\"Single Nucleotide Polymorphism database (dbSNP)\">Single Nucleotide Polymorphism database (dbSNP)<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-6\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/#nucleic-acid-database-ndb\" title=\"Nucleic Acid Database (NDB)\">Nucleic Acid Database (NDB)<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-7\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/#applications-of-nucleotide-databases\" title=\"Applications of nucleotide databases\">Applications of nucleotide databases<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-8\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/#references\" title=\"References\">References<\/a><\/li><\/ul><\/nav><\/div>\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"genbank\"><\/span><strong>GenBank<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li>GenBank is a sequence database that contains a collection of annotated nucleic acid sequence data.<\/li>\n\n\n\n<li>It includes various types of genetic material, such as genomic DNA, messenger RNA (<a href=\"https:\/\/microbenotes.com\/messenger-rna\/\" data-type=\"post\" data-id=\"29265\">mRNA<\/a>), complementary DNA (cDNA), expressed sequence tags (ESTs), high-throughput raw sequence data, and sequence polymorphisms.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"european-molecular-biology-laboratory-embl\"><\/span><strong>European Molecular Biology Laboratory (EMBL)<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li>The European Molecular Biology Laboratory (EMBL) is another nucleotide database, part of the INSDC.\u00a0<\/li>\n\n\n\n<li>It is focused on the storage and distribution of nucleotide and protein sequences.&nbsp;<\/li>\n\n\n\n<li>EMBL also develops tools to help researchers analyze and interpret this data.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"dna-data-bank-of-japan-ddbj\"><\/span><strong>DNA Data Bank of Japan (DDBJ)<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li>The DNA Data Bank of Japan (DDBJ) is another nucleotide database that exchanges data with GenBank and EMBL as a member of INSDC.<\/li>\n\n\n\n<li>DDBJ collects and exchanges nucleotide sequence data and manages bioinformatics tools for data submission and retrieval. It also develops tools for biological data analysis and organizes Bioinformatics Training Courses in Japanese.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"genome-sequence-archive-gsa\"><\/span><strong>Genome Sequence Archive (GSA)<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li>The Genome Sequence Archive (GSA) is a database that stores raw sequence data and is built based on INSDC data standards and structures.&nbsp;<\/li>\n\n\n\n<li>GSA was developed to complement the existing INSDC member databases and has now become an important tool for archiving and managing the increasing amount of genomic data.<\/li>\n\n\n\n<li>GSA accepts raw sequence reads from various sequencing platforms and stores both the sequence reads and metadata submitted by researchers worldwide.&nbsp;<\/li>\n\n\n\n<li>GSA provides free and unrestricted access to all publicly available data to scientific communities globally.&nbsp;<\/li>\n\n\n\n<li>GSA uses four primary data objects, namely BioProject, BioSample, Experiment, and Run, to organize the submitted data.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"single-nucleotide-polymorphism-database-dbsnp\"><\/span><strong>Single Nucleotide Polymorphism database (dbSNP)<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li>The Single Nucleotide Polymorphism database (dbSNP) is a public database that contains information about variations in nucleotide sequences.<\/li>\n\n\n\n<li>It is a part of the National Center for Biotechnology Information (NCBI) and is a public database that accepts entries from both public and private organizations.<\/li>\n\n\n\n<li>It stores a collection of genetic polymorphisms, including single nucleotide substitutions, deletions or insertions, and microsatellite repeat variations.&nbsp;<\/li>\n\n\n\n<li>Each entry in dbSNP includes the sequence context of the polymorphism, the occurrence frequency, and the experimental method used to detect the variation.<\/li>\n\n\n\n<li>dbSNP is open to submissions for variations from any species and genome location.&nbsp;<\/li>\n\n\n\n<li>The database supports a wide range of research areas, including physical mapping, functional analysis, pharmacogenomics, association studies, and evolutionary studies.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"nucleic-acid-database-ndb\"><\/span><strong>Nucleic Acid Database (NDB)<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li>The Nucleic Acid Database (NDB) is a collection of three-dimensional nucleic acid structures and their complexes obtained and curated from the Protein Data Bank (PDB).&nbsp;<\/li>\n\n\n\n<li>The database acts as a centralized platform for storing and accessing structural information and annotations related to nucleic acids.<\/li>\n\n\n\n<li>NDB includes annotations specific to the structure and function of nucleic acids. It also provides tools that allow users to search the database, download data and structures, analyze nucleic acids, and learn more about them.<\/li>\n\n\n\n<li>The database includes RNA and DNA oligonucleotides with two or more bases. It also includes protein-DNA and protein-RNA structures.&nbsp;<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"applications-of-nucleotide-databases\"><\/span><strong>Applications of nucleotide databases<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li>Nucleotide databases are used to identify the gene or the function of a particular nucleotide sequence by comparing an unknown sequence with the known sequences in the database.<\/li>\n\n\n\n<li>Nucleotide databases can be used to study and examine gene expression by using the sequence information stored in the databases.<\/li>\n\n\n\n<li>Nucleotide databases are also used to identify potential drug targets and develop new therapies for genetic diseases.<\/li>\n\n\n\n<li>Nucleotide databases also help in identifying genetic variations that may be linked to diseases, which ultimately helps in the development of diagnostic tools and treatments.<\/li>\n\n\n\n<li>Nucleotide databases can be used in phylogenetic analysis to analyze the evolutionary relationships between organisms, by comparing and examining their DNA or RNA sequences.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"references\"><\/span><strong>References<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ol>\n<li>Arita, M., Karsch-Mizrachi, I., &amp; Cochrane, G. (2021). The international nucleotide sequence database collaboration. Nucleic Acids Research, 49(D1), D121. https:\/\/doi.org\/10.1093\/nar\/gkaa967<\/li>\n\n\n\n<li>Berman, H. M., Gelbin, A., Clowney, L., Hsieh, H., Zardecki, C., &amp; Westbrook, J. (1996). The Nucleic Acid Database: Present and Future. Journal of Research of the National Institute of Standards and Technology, 101(3), 243-257. https:\/\/doi.org\/10.6028\/jres.101.026<\/li>\n\n\n\n<li>Bhagwat, M. (2010). Searching NCBI\u2019s dbSNP Database. Current Protocols in Bioinformatics. doi:10.1002\/0471250953.bi0119s32<\/li>\n\n\n\n<li>Birney, E. (2004). An Overview of Ensembl. Genome Research, 14(5), 925\u2013928. doi:10.1101\/gr.1860604&nbsp;<\/li>\n\n\n\n<li>Choudhuri, S. (2014). Data, Databases, Data Format, Database Search, Data Retrieval Systems, and Genome Browsers. Bioinformatics for Beginners, 77\u2013131. doi:10.1016\/b978-0-12-410471-6.00005-0<\/li>\n\n\n\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK21088\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK21088\/<\/a><\/li>\n\n\n\n<li>Sanjeev, A., Mattaparthi, V. S. K., &amp; Kaushik, S. (2018). Nucleic-Acid Structure Database. Reference Module in Life Sciences. doi:10.1016\/b978-0-12-809633-8.20285-9<\/li>\n\n\n\n<li>Wang, Y., Song, F., Zhu, J., Zhang, S., Yang, Y., Chen, T., \u2026 Zhao, W. (2017). GSA: Genome Sequence Archive *. Genomics, Proteomics &amp; Bioinformatics, 15(1), 14\u201318. doi:10.1016\/j.gpb.2017.01.001<\/li>\n\n\n\n<li>Xiong, J. (2006). Essential Bioinformatics. Cambridge: Cambridge University Press. doi:10.1017\/CBO9780511806087<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Biological databases store and organize biological data for easy retrieval of information. These centralized resources contain DNA and protein sequences and their associated information.\u00a0 Nucleotide databases are a type of &#8230; <a title=\"Nucleotide Databases- Definition, Types, Examples, Uses\" class=\"read-more\" href=\"https:\/\/microbenotes.com\/nucleotide-sequences-database\/\" aria-label=\"Read more about Nucleotide Databases- Definition, Types, Examples, Uses\">Read more<\/a><\/p>\n","protected":false},"author":27,"featured_media":40896,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[6212],"tags":[4016,4013,4012,4015,4011,4008,4007,4014,4010,4009],"custom":{"td_video":"","featured_image":"https:\/\/microbenotes.com\/wp-content\/uploads\/2023\/04\/Nucleotide-Databases.jpg","author":{"name":"Sanju Tamang","avatar":"https:\/\/secure.gravatar.com\/avatar\/f337d733e7b15ac78c15677d4185c8ef?s=96&d=mm&r=g"},"categories":[{"term_id":6212,"name":"Bioinformatics","slug":"bioinformatics","term_group":0,"term_taxonomy_id":6212,"taxonomy":"category","description":"<strong>Bioinformatics is an emerging field of science that deals with the application of computers to the collection, organization, analysis, manipulation, presentation, and sharing of biological data.<\/strong>\r\n<ul>\r\n \t<li>Bioinformatics is an interdisciplinary field directly involving molecular biology, genetics, computer science, mathematics, and statistics.<\/li>\r\n \t<li>The central component of bioinformatics is the study of the best ways to design and operate biologic databases.<\/li>\r\n \t<li>As a large amount of nucleotide and protein sequence data are obtained via various research techniques, along with other types of information stored in primary and secondary biological databases, scientists started to use computers to obtain and analyze biological data in their daily research with bioinformatics tools.<\/li>\r\n \t<li>To help the biologists access the databases effectively and use the analysis tools efficiently, bioinformatics has eventually become a vital part of biological education.<\/li>\r\n \t<li>Bioinformatics is an evolving discipline, and complex software programs are now being used for retrieving, sorting out, analyzing, predicting, and storing DNA and protein sequence data.<\/li>\r\n \t<li>One of the fundamental activities in bioinformatics is the sequence analysis of DNA and proteins using various programs and databases available on the world wide web.<\/li>\r\n \t<li>Large commercial enterprises such as pharmaceutical companies employ bioinformaticians to perform and maintain the large scale and complex bioinformatics needs of these industries.<\/li>\r\n \t<li>Apart from the analysis of genome sequence data, bioinformatics is now being used for a vast array of other vital tasks, including analysis of gene variation and expression, analysis, and prediction of gene and protein structure and function.<\/li>\r\n \t<li>Besides, bioinformatics has found its importance in tasks like prediction and detection of gene regulation networks and presentation and analysis of molecular pathways in order to understand gene-disease interactions.<\/li>\r\n \t<li>Bioinformatics even has clinical applications as the whole genome sequencing of an organism allows for the production of a complete list of human gene products that may provide new drugs and gene therapy for single-gene diseases may become routine.<\/li>\r\n \t<li>Bioinformatics can be used for different other fields of the biology of different groups of living beings.<\/li>\r\n<\/ul>","parent":0,"count":21,"filter":"raw","cat_ID":6212,"category_count":21,"category_description":"<strong>Bioinformatics is an emerging field of science that deals with the application of computers to the collection, organization, analysis, manipulation, presentation, and sharing of biological data.<\/strong>\r\n<ul>\r\n \t<li>Bioinformatics is an interdisciplinary field directly involving molecular biology, genetics, computer science, mathematics, and statistics.<\/li>\r\n \t<li>The central component of bioinformatics is the study of the best ways to design and operate biologic databases.<\/li>\r\n \t<li>As a large amount of nucleotide and protein sequence data are obtained via various research techniques, along with other types of information stored in primary and secondary biological databases, scientists started to use computers to obtain and analyze biological data in their daily research with bioinformatics tools.<\/li>\r\n \t<li>To help the biologists access the databases effectively and use the analysis tools efficiently, bioinformatics has eventually become a vital part of biological education.<\/li>\r\n \t<li>Bioinformatics is an evolving discipline, and complex software programs are now being used for retrieving, sorting out, analyzing, predicting, and storing DNA and protein sequence data.<\/li>\r\n \t<li>One of the fundamental activities in bioinformatics is the sequence analysis of DNA and proteins using various programs and databases available on the world wide web.<\/li>\r\n \t<li>Large commercial enterprises such as pharmaceutical companies employ bioinformaticians to perform and maintain the large scale and complex bioinformatics needs of these industries.<\/li>\r\n \t<li>Apart from the analysis of genome sequence data, bioinformatics is now being used for a vast array of other vital tasks, including analysis of gene variation and expression, analysis, and prediction of gene and protein structure and function.<\/li>\r\n \t<li>Besides, bioinformatics has found its importance in tasks like prediction and detection of gene regulation networks and presentation and analysis of molecular pathways in order to understand gene-disease interactions.<\/li>\r\n \t<li>Bioinformatics even has clinical applications as the whole genome sequencing of an organism allows for the production of a complete list of human gene products that may provide new drugs and gene therapy for single-gene diseases may become routine.<\/li>\r\n \t<li>Bioinformatics can be used for different other fields of the biology of different groups of living beings.<\/li>\r\n<\/ul>","cat_name":"Bioinformatics","category_nicename":"bioinformatics","category_parent":0}]},"_links":{"self":[{"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/posts\/40897"}],"collection":[{"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/users\/27"}],"replies":[{"embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/comments?post=40897"}],"version-history":[{"count":0,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/posts\/40897\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/media\/40896"}],"wp:attachment":[{"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/media?parent=40897"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/categories?post=40897"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/tags?post=40897"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}