{"id":41622,"date":"2023-08-03T15:04:37","date_gmt":"2023-08-03T09:19:37","guid":{"rendered":"https:\/\/microbenotes.com\/blast-bioinformatics\/"},"modified":"2023-08-03T15:04:37","modified_gmt":"2023-08-03T09:19:37","slug":"blast-bioinformatics","status":"publish","type":"post","link":"https:\/\/microbenotes.com\/blast-bioinformatics\/","title":{"rendered":"BLAST (Bioinformatics)- Definition, 5 Types, Steps, Uses"},"content":{"rendered":"\n<p>With the increase in DNA and protein sequence <a href=\"https:\/\/microbenotes.com\/biological-databases-types-and-importance\/\" data-type=\"post\" data-id=\"1691\">databases<\/a>, there is a growing need for more faster and efficient methods to analyze this large amount of data. One of the most commonly used bioinformatics tools today to study DNA and protein sequences is called BLAST.\u00a0<\/p>\n\n\n\n<p><strong>BLAST stands for Basic Local Alignment Search Tool.<\/strong> It is a widely used bioinformatics program that was first introduced by Stephen Altschul et al. in 1990 and has since become one of the most popular tools for sequence similarity search.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" src=\"https:\/\/microbenotes.com\/wp-content\/uploads\/2022\/07\/Basic-Local-Alignment-Search-Tool-BLAST.jpg\" alt=\"Basic Local Alignment Search Tool (BLAST)\" class=\"wp-image-38623\"\/><figcaption class=\"wp-element-caption\">Basic Local Alignment Search Tool (BLAST). Image Source: <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi\" target=\"_blank\" rel=\"noreferrer noopener\">NCBI<\/a>.<\/figcaption><\/figure>\n\n\n\n<p><strong>BLAST is a powerful tool for analyzing biological sequence data. <\/strong>Since the initial release of BLAST in 1990, it has undergone continuous updates to improve its speed and accuracy. BLAST is now considered a crucial and widely used tool in the field of bioinformatics. It has played a vital role in numerous research studies and has paved the way for the development of other sequence comparison tools.<\/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\/blast-bioinformatics\/#5-types-of-blast\" title=\"5 Types of BLAST\">5 Types of BLAST<\/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\/blast-bioinformatics\/#how-blast-works\" title=\"How BLAST Works\">How BLAST Works<\/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\/blast-bioinformatics\/#characteristics-of-blast\" title=\"Characteristics of BLAST\">Characteristics of BLAST<\/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\/blast-bioinformatics\/#applications-of-blast\" title=\"Applications of BLAST\">Applications of BLAST<\/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\/blast-bioinformatics\/#references\" title=\"References\">References<\/a><\/li><\/ul><\/nav><\/div>\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"5-types-of-blast\"><\/span><strong>5 Types of BLAST<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p>There are five types (variants) of BLAST that are differentiated based on the type of sequence (DNA or protein) of the query and database sequences.<\/p>\n\n\n\n<ol>\n<li><strong>BLASTN<\/strong> compares a nucleotide query sequence to a nucleotide sequence database.<\/li>\n\n\n\n<li><strong>BLASTP<\/strong> compares a protein query sequence to a protein sequence database.<\/li>\n\n\n\n<li><strong>BLASTX <\/strong>compares a nucleotide query sequence to a protein sequence database by translating the query sequence into its six possible reading frames and aligning them with the protein sequences.\u00a0<\/li>\n\n\n\n<li><strong>TBLASTN<\/strong> compares a protein query sequence to a nucleotide sequence database by translating the nucleotide sequences in all six reading frames and aligning them with the protein sequence.<\/li>\n\n\n\n<li><strong>TBLASTX<\/strong> compares a nucleotide query sequence to a nucleotide sequence database by translating the query sequence in all six reading frames and aligning them with the nucleotide sequences.<\/li>\n<\/ol>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"how-blast-works\"><\/span><strong>How BLAST Works<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p>BLAST works by comparing a query sequence to a database of sequences to find regions of similarity. It uses a heuristic approach to search for similarities in the database, making it faster and more efficient.<\/p>\n\n\n\n<p>BLAST performs sequence alignment through the following steps.&nbsp;<\/p>\n\n\n\n<ul>\n<li><strong>Step 1: <\/strong>The first step is to create a lookup table or list of words from the query sequence. This step is also called seeding. First, BLAST takes the query sequence and breaks it into short segments called words. For protein sequences, each word is usually three amino acids long, and for DNA sequences, each word is usually eleven nucleotides long.<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" src=\"https:\/\/microbenotes.com\/wp-content\/uploads\/2023\/03\/How-BLAST-Works.jpg\" alt=\"How BLAST Works\" class=\"wp-image-40204\"\/><figcaption class=\"wp-element-caption\"><strong>How BLAST Works- Step 1. Image Source: <a href=\"https:\/\/www.nlm.nih.gov\/ncbi\/workshops\/2022-10_Basic-Web-BLAST\/how-blast-works.html\" target=\"_blank\" data-type=\"URL\" data-id=\"https:\/\/www.nlm.nih.gov\/ncbi\/workshops\/2022-10_Basic-Web-BLAST\/how-blast-works.html\" rel=\"noreferrer noopener\">NLM, NCBI<\/a>.<\/strong><\/figcaption><\/figure>\n\n\n\n<ul>\n<li><strong>Step 2: <\/strong>The second step is to search a database of known sequences to find any sequences that contain the same words as the query sequence. This is done to identify database sequences containing the matching words.<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" src=\"https:\/\/microbenotes.com\/wp-content\/uploads\/2023\/03\/How-BLAST-Works-Step-1.jpg\" alt=\"How BLAST Works- Step 2\" class=\"wp-image-40205\"\/><figcaption class=\"wp-element-caption\"><strong>How BLAST Works- Step 2. Image Source: <a href=\"https:\/\/www.nlm.nih.gov\/ncbi\/workshops\/2022-10_Basic-Web-BLAST\/how-blast-works.html\" target=\"_blank\" data-type=\"URL\" data-id=\"https:\/\/www.nlm.nih.gov\/ncbi\/workshops\/2022-10_Basic-Web-BLAST\/how-blast-works.html\" rel=\"noreferrer noopener\">NLM, NCBI<\/a>.<\/strong><\/figcaption><\/figure>\n\n\n\n<ul>\n<li><strong>Step 3: <\/strong>BLAST then scores the similarity of the matching words. The matching of the words is scored by a given substitution matrix. If a word is above a certain threshold, it is considered a match.\u00a0<br>Two commonly used substitution matrices for protein sequences are PAM (Percent Accepted Mutations) and BLOSUM (Blocks Substitution Matrix). For nucleotide sequences, the scoring matrix is based on match-mismatch scoring.<\/li>\n\n\n\n<li><strong>Step 4:<\/strong> The fourth step involves pairwise alignment by extending the words in both directions while counting the alignment score using the same substitution matrix. If the score drops below a certain threshold due to differences in the sequences or mismatches, the alignment stops. The resulting aligned segment pair without gaps is called the high-scoring segment pair (HSP).<\/li>\n<\/ul>\n\n\n\n<p>BLAST also calculates a statistical significance value for each alignment. It is called E-value or Expect value. The E-value represents the probability of obtaining a sequence match by random chance. A lower E-value indicates that the sequence match is less likely to be a result of random occurrence. Hence, the lower the E-value, the higher the level of significance.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"characteristics-of-blast\"><\/span><strong>Characteristics of BLAST<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p>Several key features of BLAST make it a widely used tool in bioinformatics. Some of these are:<\/p>\n\n\n\n<ul>\n<li>BLAST is fast and efficient, making it possible to handle large databases of sequences.<\/li>\n\n\n\n<li>It is a flexible and versatile tool as it can be used to search for similarities in both nucleotide and protein sequences.<\/li>\n\n\n\n<li>It is highly sensitive which allows the identification of even small similarities between sequences.<\/li>\n\n\n\n<li>It aims to identify regions of local similarity between the query sequence and the database sequence, rather than attempting to align the entire sequences.<\/li>\n\n\n\n<li>It has a user-friendly interface that makes it easy to input query sequences and interpret the results.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"applications-of-blast\"><\/span><strong>Applications of BLAST<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p>BLAST has a wide range of applications. Some of the most common applications are:<\/p>\n\n\n\n<ul>\n<li>BLAST can be used to identify unknown sequences by comparing them with known sequences in a database which helps in predicting the functions of proteins or genes.<\/li>\n\n\n\n<li>BLAST can also be used in phylogenetic analysis which is important for understanding the evolutionary relationships between different species.<\/li>\n\n\n\n<li>BLAST can also be used to identify functionally conserved domains within proteins which is important for predicting the functions of proteins.<\/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>BLAST QuickStart &#8211; Comparative Genomics &#8211; NCBI Bookshelf (nih.gov)<\/li>\n\n\n\n<li>BLAST: Basic Local Alignment Search Tool (nih.gov)<\/li>\n\n\n\n<li>BLAST: Compare &amp; identify sequences &#8211; NCBI Bioinformatics Resources: An Introduction &#8211; Library Guides at UC Berkeley<\/li>\n\n\n\n<li>Grzegorz M. Boratyn, Christiam Camacho, Peter S. Cooper, George Coulouris, Amelia Fong, Ning Ma, Thomas L. Madden, Wayne T. Matten, Scott D. McGinnis, Yuri Merezhuk, Yan Raytselis, Eric W. Sayers, Tao Tao, Jian Ye, Irena Zaretskaya, BLAST: a more efficient report with usability improvements, Nucleic Acids Research, Volume 41, Issue W1, 1 July 2013, Pages W29\u2013W33, https:\/\/doi.org\/10.1093\/nar\/gkt282<\/li>\n\n\n\n<li>How BLAST Works (nih.gov)<\/li>\n\n\n\n<li>McGinnis, S., &amp; Madden, T. L. (2004). BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Research, 32(Web Server issue), W20. https:\/\/doi.org\/10.1093\/nar\/gkh435<\/li>\n\n\n\n<li>NCBI_blast.pdf (unmc.edu)<\/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>With the increase in DNA and protein sequence databases, there is a growing need for more faster and efficient methods to analyze this large amount of data. One of the &#8230; <a title=\"BLAST (Bioinformatics)- Definition, 5 Types, Steps, Uses\" class=\"read-more\" href=\"https:\/\/microbenotes.com\/blast-bioinformatics\/\" aria-label=\"Read more about BLAST (Bioinformatics)- Definition, 5 Types, Steps, Uses\">Read more<\/a><\/p>\n","protected":false},"author":27,"featured_media":41619,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[6212],"tags":[3693,6378],"custom":{"td_video":"","featured_image":"https:\/\/microbenotes.com\/wp-content\/uploads\/2022\/07\/Basic-Local-Alignment-Search-Tool-BLAST.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\/41622"}],"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=41622"}],"version-history":[{"count":0,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/posts\/41622\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/media\/41619"}],"wp:attachment":[{"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/media?parent=41622"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/categories?post=41622"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/tags?post=41622"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}