{"id":41462,"date":"2023-08-03T15:02:53","date_gmt":"2023-08-03T09:17:53","guid":{"rendered":"https:\/\/microbenotes.com\/fasta-and-blast\/"},"modified":"2023-08-03T22:19:52","modified_gmt":"2023-08-03T16:34:52","slug":"fasta-and-blast","status":"publish","type":"post","link":"https:\/\/microbenotes.com\/fasta-and-blast\/","title":{"rendered":"What are FASTA and BLAST? An Introduction"},"content":{"rendered":"\n<ul>\n<li><span style=\"color: #000000;\">The number of DNA and protein sequences in public databases is very large.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">Searching a database involves aligning the query sequence to each sequence in the database, to find significant local alignment.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">BLAST and FASTA are two similarity searching programs that identify homologous DNA sequences and proteins based on the excess sequence similarity.&nbsp;<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">They provide facilities for comparing DNA and proteins sequences with the existing DNA and protein databases.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">They are two major <strong>heuristic algorithms<\/strong> for performing database searches.<\/span><\/li>\n<\/ul>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter\"><img decoding=\"async\" src=\"https:\/\/microbenotes.com\/wp-content\/uploads\/2019\/02\/BLAST.jpg\" alt=\"BLAST\" class=\"wp-image-1826\"\/><\/figure><\/div>\n\n\n<p><span style=\"color: #000000;\"><\/span><\/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\/fasta-and-blast\/#working-of-fasta-and-blast\" title=\"Working of FASTA and BLAST\">Working of FASTA and 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\/fasta-and-blast\/#blast-basic-local-alignment-search-tool\" title=\"BLAST (Basic Local Alignment Search Tool)\">BLAST (Basic Local Alignment Search Tool)<\/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\/fasta-and-blast\/#variants-of-blast\" title=\"Variants of BLAST \">Variants 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\/fasta-and-blast\/#fasta\" title=\"FASTA \">FASTA <\/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\/fasta-and-blast\/#references\" title=\"References\">References<\/a><\/li><\/ul><\/nav><\/div>\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"working-of-fasta-and-blast\"><\/span><span style=\"color: #000000;\"><strong>Working of FASTA and BLAST<\/strong><\/span><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li><span style=\"color: #000000;\">FASTA and BLAST&nbsp;are the software tools used in bioinformatics. Both BLAST and FASTA use a heuristic word method for fast pairwise sequence alignment.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">It works by finding short stretches of identical or nearly identical letters in two sequences. These short strings of characters are called words.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">The basic assumption is that two related sequences must have at least one word in common.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">By first identifying word matches, a longer alignment can be obtained by extending similarity regions from the words.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">Once regions of high sequence similarity are found, adjacent high-scoring regions can be joined into a full alignment.<\/span><\/li>\n<\/ul>\n\n\n\n<p><span style=\"color: #000000;\">The&nbsp;main difference&nbsp;between BLAST and FASTA is that&nbsp;BLAST is mostly involved in finding of ungapped, locally optimal sequence alignments&nbsp;whereas&nbsp;FASTA is involved in finding similarities between less similar sequences.<\/span><\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"blast-basic-local-alignment-search-tool\"><\/span><span style=\"color: #000000;\"><strong>BLAST (Basic Local Alignment Search Tool)<\/strong><\/span><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li><span style=\"color: #000000;\">The BLAST program was developed by Stephen Altschul of NCBI in 1990 and has since become one of the most popular programs for sequence analysis.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">BLAST uses heuristics to align a query sequence with all sequences in a database.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">The objective is to find high-scoring ungapped segments among related sequences. The existence of such segments above a given threshold indicates pairwise similarity beyond random chance, which helps to discriminate related sequences from unrelated sequences in a database.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">BLAST is popular as a bioinformatics tool due to its ability to identify regions of local similarity between two sequences quickly. BLAST calculates an expectation value, which estimates the number of matches between two sequences. It uses the local alignment of sequences.<\/span><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"variants-of-blast\"><\/span><span style=\"color: #000000;\"><strong>Variants of BLAST <\/strong><\/span><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li><span style=\"color: #000000;\"><strong>BLAST-N:<\/strong> compares nucleotide sequence with nucleotide sequences<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\"><strong>BLAST-P:<\/strong> compares protein sequences with protein sequences<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\"><strong>BLAST-X:<\/strong> Compares nucleotide sequences against the protein sequences<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\"><strong>tBLAST-N<\/strong>: compares the protein sequences against the six frame translations of nucleotide sequences<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\"><strong>tBLAST-X:<\/strong> Compares the six frame translations of nucleotide sequence against the six frame translations of protein sequences.<\/span><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"fasta\"><\/span><span style=\"color: #000000;\"><strong>FASTA <\/strong><\/span><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ul>\n<li><span style=\"color: #000000;\">FASTA stands for fast-all\u201d or \u201cFastA\u201d.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">It was the first database similarity search tool developed, preceding the development of BLAST.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">FASTA is another sequence alignment tool which is used to search similarities between sequences of DNA and proteins.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">FASTA uses a \u201chashing\u201d strategy to find matches for a short stretch of identical residues with a length of k. The string of residues is known as ktuples or ktups, which are equivalent to words in BLAST, but are normally shorter than the words.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">Typically, a ktup is composed of two residues for protein sequences and six residues for DNA sequences.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">The query sequence is thus broken down into sequence patterns or words known as k-tuples and the target sequences are searched for these k-tuples in order to find the similarities between the two.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">FASTA is a fine tool for similarity searches.&nbsp;<\/span><\/li>\n<\/ul>\n\n\n\n<p><span style=\"color: #000000;\">These methods are not guaranteed to find the optimal alignment or true homologs, but are 50\u2013100 times faster than dynamic programming.<\/span><\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"references\"><\/span><span style=\"color: #000000;\"><strong>References<\/strong><\/span><span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<ol>\n<li><span style=\"color: #000000;\">Xiong J. (2006). Essential Bioinformatics. Texas A &amp; M University. Cambridge University Press.<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">Arthur M Lesk (2014). Introduction to bioinformatics. Oxford University Press. Oxford, United Kingdom<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">http:\/\/pediaa.com\/difference-between-blast-and-fasta\/#BLAST<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">https:\/\/embnet.vital-it.ch\/CoursEMBnet\/Basel03\/slides\/BLAST_FASTA.pdf<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">https:\/\/www.slideshare.net\/avrilcoghlan\/blast-16572940<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">https:\/\/www.cs.helsinki.fi\/bioinformatiikka\/mbi\/courses\/0708\/itb\/slides\/itb0708_slides_83-116.pdf<\/span><\/li>\n\n\n\n<li><span style=\"color: #000000;\">https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=BlastHelp<\/span><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Working of FASTA and BLAST The&nbsp;main difference&nbsp;between BLAST and FASTA is that&nbsp;BLAST is mostly involved in finding of ungapped, locally optimal sequence alignments&nbsp;whereas&nbsp;FASTA is involved in finding similarities between less &#8230; <a title=\"What are FASTA and BLAST? An Introduction\" class=\"read-more\" href=\"https:\/\/microbenotes.com\/fasta-and-blast\/\" aria-label=\"Read more about What are FASTA and BLAST? An Introduction\">Read more<\/a><\/p>\n","protected":false},"author":1,"featured_media":41461,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[6212],"tags":[3696,3693,3698,3699,3700,3692,3694,3695,3701,3702,3697],"custom":{"td_video":"","featured_image":"https:\/\/microbenotes.com\/wp-content\/uploads\/2019\/02\/BLAST.jpg","author":{"name":"Sagar Aryal","avatar":"https:\/\/secure.gravatar.com\/avatar\/862472ea06500d4318f1ad82addb608e?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\/41462"}],"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\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/comments?post=41462"}],"version-history":[{"count":0,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/posts\/41462\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/media\/41461"}],"wp:attachment":[{"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/media?parent=41462"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/categories?post=41462"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/microbenotes.com\/wp-json\/wp\/v2\/tags?post=41462"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}