{"id":1630,"date":"2023-03-30T00:34:50","date_gmt":"2023-03-29T15:34:50","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=1630"},"modified":"2023-03-30T00:57:33","modified_gmt":"2023-03-29T15:57:33","slug":"pairwise-sequence-alignment","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/pairwise-sequence-alignment\/","title":{"rendered":"Pairwise sequence alignment"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Introduction<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Sequence alignment<\/strong>, which involves aligning two sequences and measuring matches and mismatches of characters, is a way to quantify the similarity between two sequences. The alignment is the procedure of finding two <strong>extended sequences<\/strong> with the same length from the two sequences, where an extended sequence is generated by inserting null characters &#8216;-&#8216; into the original sequences. A pair of two extended sequences with the same length is an <strong>alignment <\/strong>of the two sequences. An <strong>alignment score <\/strong>is calculated for an alignment by assigning scores for matches, mismatches, and gaps. <strong>Sequence alignment<\/strong> is the procedure of finding the <strong>optimal alignment<\/strong> with the <strong>highest alignment score<\/strong>. <\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Method <\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Pseudo code<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Input: two sequences<\/li>\n\n\n\n<li>Output: alignment score matrix<\/li>\n<\/ul>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Retrieve length of the sequence (m, n)<\/li>\n\n\n\n<li>Create an empty alignment score matrix (m x n)<\/li>\n\n\n\n<li>Calculate the alignment score at the first row<\/li>\n\n\n\n<li>Calculate the alignment score at the first column<\/li>\n\n\n\n<li>Calculate alignment score row by row<\/li>\n\n\n\n<li>Print the result<\/li>\n<\/ol>\n\n\n\n<h2 class=\"wp-block-heading\">Implementation with Python code<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">The path graph score table can be calculated in numerous ways. For educational purpose, a simple and intuitive implementation code is is introduced here.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>1. Definition of parameters and substitution score matrix<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Substitution score is defined to calculate the alignment score of matches and mismatches. Here, an identity matrix is used for the substitution matrix.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\"># substitution matrix\r\nsubmat = {('A', 'A'): 1, ('A', 'T'): 0, ('A', 'G'): 0, ('A', 'C'): 0,\r\n          ('T', 'A'): 0, ('T', 'T'): 1, ('T', 'G'): 0, ('T', 'C'): 0,\r\n          ('G', 'A'): 0, ('G', 'T'): 0, ('G', 'G'): 1, ('G', 'C'): 0,\r\n          ('C', 'A'): 0, ('C', 'T'): 0, ('C', 'G'): 0, ('C', 'C'): 1\r\n         }\r\ngap_score = -1<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>2. Set input sequences &amp; retrieve length of the sequences<\/strong><\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\"># Set input sequences \ns = \"ACGC\"\r\nt = \"GACTAC\"\n\n# Retrieve the lengths of the sequences \nm = len(s)\r\nn = len(t)<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>3. Create an empty aligment score matrix <\/strong><\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">mat = []   # alginment score matrix\r\nfor i in range(m+1):\r\n    mat.append([0] * (n+1))<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>4. Fill in the first row and the first column<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">The first row and the first column represent extended sequences started with gaps in the first and the sequence sequences. The alignment score of the other nodes depends on these scores, so they were calculated first. <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\"># first row\r\nfor i in range(n):\r\n    mat[0][i+1] = mat[0][i] + gap_score\r\n\r\n# first column\r\nfor i in range(m):\r\n    mat[i+1][0] = mat[i][0] + gap_score<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>5. Fill in the alignment score matrix <\/strong><\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">for i in range(m):\r\n    for j in range(n):\r\n        mx = max(mat[i][j] + submat[(s[i], t[j])], \r\n                 mat[i][j+1] + gap_score, \r\n                 mat[i+1][j] + gap_score)\r\n        mat[i+1][j+1] = mx<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>6. Print the results<\/strong><\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\"># Print the result\nprint(mat)\n\n# Print the result with better representation \nimport pandas as pd\r\nmat = pd.DataFrame(mat, index= ['-'] + list(s), columns = ['-'] + list(t))\r\nprint(mat)<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Introduction Sequence alignment, which involves aligning two sequences and measuring matches and mismatches of characters, is a way to quantify the similarity between two sequences. The alignment is the procedure of finding two extended sequences with the same length from the two sequences, where an extended sequence is generated by inserting null characters &#8216;-&#8216; into [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":"","_members_access_role":[],"_members_access_error":""},"categories":[1],"tags":[],"class_list":["post-1630","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.4 - 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The alignment is the procedure of finding two extended sequences with the same length from the two sequences, where an extended sequence is generated by inserting null characters &#8216;-&#8216; into&hellip;","_links":{"self":[{"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/posts\/1630","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/comments?post=1630"}],"version-history":[{"count":3,"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/posts\/1630\/revisions"}],"predecessor-version":[{"id":2097,"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/posts\/1630\/revisions\/2097"}],"wp:attachment":[{"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/media?parent=1630"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/categories?post=1630"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-json\/wp\/v2\/tags?post=1630"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}