{"id":254603,"date":"2024-05-21T00:37:17","date_gmt":"2024-05-21T00:37:17","guid":{"rendered":"https:\/\/namso-gen.co\/blog\/?p=254603"},"modified":"2024-05-21T00:37:17","modified_gmt":"2024-05-21T00:37:17","slug":"what-is-e-value-in-blast","status":"publish","type":"post","link":"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/","title":{"rendered":"What is e value in BLAST?"},"content":{"rendered":"<p>**What is e value in BLAST?**<\/p>\n<p>The e value, also known as the expectation value, is a statistical parameter that measures the likelihood of obtaining a given alignment score by chance in BLAST (Basic Local Alignment Search Tool). It provides an estimate of the number of similar sequences expected to be found by chance in a given database when searching with a particular query sequence.<\/p>\n<p>The e value is an essential metric in BLAST that helps researchers assess the biological significance of a sequence similarity. It helps distinguish matches that are merely coincidental from those that are more likely to have a functional or evolutionary relationship. A lower e value indicates a more significant alignment and suggests a higher probability of a biologically relevant match.<\/p>\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_62 counter-hierarchy ez-toc-counter ez-toc-grey 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: #999;color:#999\" 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: #999;color:#999\" 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-3'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#FAQs_about_e_value_in_BLAST\" title=\"FAQs about e value in BLAST:\">FAQs about e value in BLAST:<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#1_How_is_the_e_value_calculated_in_BLAST\" title=\"1. How is the e value calculated in BLAST?\">1. How is the e value calculated in BLAST?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#2_What_is_the_significance_of_an_e_value\" title=\"2. What is the significance of an e value?\">2. What is the significance of an e value?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#3_What_e_value_cutoff_should_be_used_in_BLAST_searches\" title=\"3. What e value cutoff should be used in BLAST searches?\">3. What e value cutoff should be used in BLAST searches?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#4_Can_the_e_value_be_used_to_determine_the_strength_of_a_biological_relationship\" title=\"4. Can the e value be used to determine the strength of a biological relationship?\">4. Can the e value be used to determine the strength of a biological relationship?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-6\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#5_How_does_the_e_value_relate_to_sequence_identity\" title=\"5. How does the e value relate to sequence identity?\">5. How does the e value relate to sequence identity?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-7\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#6_Can_the_e_value_be_zero_in_BLAST\" title=\"6. Can the e value be zero in BLAST?\">6. Can the e value be zero in BLAST?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-8\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#7_Does_a_higher_e_value_imply_a_weaker_similarity\" title=\"7. Does a higher e value imply a weaker similarity?\">7. Does a higher e value imply a weaker similarity?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-9\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#8_Is_the_e_value_affected_by_the_size_of_the_database\" title=\"8. Is the e value affected by the size of the database?\">8. Is the e value affected by the size of the database?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-10\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#9_What_is_the_relationship_between_significance_threshold_and_e_value\" title=\"9. What is the relationship between significance threshold and e value?\">9. What is the relationship between significance threshold and e value?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-11\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#10_Can_the_e_value_be_used_to_compare_sequences_between_different_searches\" title=\"10. Can the e value be used to compare sequences between different searches?\">10. Can the e value be used to compare sequences between different searches?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-12\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#11_Is_BLAST_the_only_biological_tool_that_uses_e_values\" title=\"11. Is BLAST the only biological tool that uses e values?\">11. Is BLAST the only biological tool that uses e values?<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-13\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#12_Can_a_high-scoring_alignment_have_a_high_e_value\" title=\"12. Can a high-scoring alignment have a high e value?\">12. Can a high-scoring alignment have a high e value?<\/a><\/li><\/ul><\/nav><\/div>\n<h3><span class=\"ez-toc-section\" id=\"FAQs_about_e_value_in_BLAST\"><\/span>FAQs about e value in BLAST:<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<h3><span class=\"ez-toc-section\" id=\"1_How_is_the_e_value_calculated_in_BLAST\"><\/span>1. How is the e value calculated in BLAST?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nThe e value is calculated based on the size of the database searched, the alignment score, and the length of the query sequence. It is derived using statistical models that consider the probability of obtaining a given score by chance.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"2_What_is_the_significance_of_an_e_value\"><\/span>2. What is the significance of an e value?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nThe e value indicates the expected number of sequences with similar alignment scores that would occur by chance. A lower e value suggests a higher likelihood of a meaningful relationship between the query sequence and the hit.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"3_What_e_value_cutoff_should_be_used_in_BLAST_searches\"><\/span>3. What e value cutoff should be used in BLAST searches?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nThe choice of an appropriate e value threshold depends on the specific study, database size, and the desired level of stringency. A common threshold is 0.01, which implies that an alignment score as extreme as or more extreme than the observed score would occur by chance in only 1% of the database sequences.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"4_Can_the_e_value_be_used_to_determine_the_strength_of_a_biological_relationship\"><\/span>4. Can the e value be used to determine the strength of a biological relationship?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nThe e value alone cannot determine the strength of a biological relationship. It is merely a statistical measure that provides a preliminary assessment of the significance of a sequence similarity. Additional analyses are usually required to confirm and interpret the relationship.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"5_How_does_the_e_value_relate_to_sequence_identity\"><\/span>5. How does the e value relate to sequence identity?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nThe e value and sequence identity are distinct parameters. While sequence identity reflects the similarity between two sequences in terms of identical residues, the e value estimates the likelihood of obtaining a given alignment solely by chance.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"6_Can_the_e_value_be_zero_in_BLAST\"><\/span>6. Can the e value be zero in BLAST?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nTechnically, the e value cannot be zero in BLAST. However, it can be very close to zero, which suggests an extremely significant alignment between the query and hit sequences.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"7_Does_a_higher_e_value_imply_a_weaker_similarity\"><\/span>7. Does a higher e value imply a weaker similarity?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nYes, a higher e value indicates a weaker similarity. A larger e value suggests that the observed alignment score is more likely to have occurred by chance, reducing the confidence in the biological significance of the match.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"8_Is_the_e_value_affected_by_the_size_of_the_database\"><\/span>8. Is the e value affected by the size of the database?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nYes, the size of the database directly affects the e value calculation. A larger database increases the space for chance matches, thus potentially increasing the e value.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"9_What_is_the_relationship_between_significance_threshold_and_e_value\"><\/span>9. What is the relationship between significance threshold and e value?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nThe significance threshold is often set based on an acceptable e value or a desired level of significance. A stricter threshold requires a lower e value, increasing the stringency of the search.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"10_Can_the_e_value_be_used_to_compare_sequences_between_different_searches\"><\/span>10. Can the e value be used to compare sequences between different searches?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nThe e value is specific to a particular search and database combination. It cannot be directly used to compare sequences from different searches with distinct databases.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"11_Is_BLAST_the_only_biological_tool_that_uses_e_values\"><\/span>11. Is BLAST the only biological tool that uses e values?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nNo, e values are commonly used in other sequence analysis tools as well. Tools like HMMER and PSI-BLAST also utilize e values to assess the significance of sequence alignments.<\/p>\n<h3><span class=\"ez-toc-section\" id=\"12_Can_a_high-scoring_alignment_have_a_high_e_value\"><\/span>12. Can a high-scoring alignment have a high e value?<span class=\"ez-toc-section-end\"><\/span><\/h3>\n<p>\nYes, a high-scoring alignment can have a high e value. It could indicate that the observed alignment score is likely to occur by chance within the database, rather than suggesting a meaningful biological relationship.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>**What is e value in BLAST?** The e value, also known as the expectation value, is a statistical parameter that measures the likelihood of obtaining a given alignment score by chance in BLAST (Basic Local Alignment Search Tool). It provides an estimate of the number of similar sequences expected to be found by chance in &#8230; <\/p>\n<p class=\"read-more-container\"><a title=\"What is e value in BLAST?\" class=\"read-more button\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/#more-254603\">Read more<span class=\"screen-reader-text\">What is e value in BLAST?<\/span><\/a><\/p>\n","protected":false},"author":64,"featured_media":107420,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[86279],"tags":[],"class_list":["post-254603","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-learn","no-featured-image-padding"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v22.1 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>What is e value in BLAST?<\/title>\n<meta name=\"description\" content=\"**What is e value in BLAST?** The e value, also known as the expectation value, is a statistical parameter that measures the likelihood of obtaining a\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"What is e value in BLAST?\" \/>\n<meta property=\"og:description\" content=\"**What is e value in BLAST?** The e value, also known as the expectation value, is a statistical parameter that measures the likelihood of obtaining a\" \/>\n<meta property=\"og:url\" content=\"https:\/\/namso-gen.co\/blog\/what-is-e-value-in-blast\/\" \/>\n<meta property=\"og:site_name\" content=\"Namso Gen Blog - 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