{"id":4632,"date":"2026-04-15T09:52:41","date_gmt":"2026-04-15T00:52:41","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=4632"},"modified":"2026-04-15T09:57:36","modified_gmt":"2026-04-15T00:57:36","slug":"activity-multiple-sequence-alignment","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/activity-multiple-sequence-alignment\/","title":{"rendered":"Activity for Multiple Sequence Alignment"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Introduction<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">\ubcf8 \uc2e4\uc2b5\uc5d0\uc11c\ub294 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4\uc744 \uc218\uc9d1\ud558\uace0, Multiple Sequence Alignment (MSA)\ub97c \uc218\ud589\ud558\uc5ec<br>\uc11c\uc5f4 \uac04\uc758 \ubcf4\uc874 \uc601\uc5ed(conserved region)\uacfc \uac00\ubcc0 \uc601\uc5ed(variable region)\uc744 \ubd84\uc11d\ud55c\ub2e4.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Multiple sequence alignment \uc218\ud589<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">\uc2e4\uc2b5 \ub514\ub809\ud1a0\ub9ac \uad6c\uc131<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uc2e4\uc2b5 \ub514\ub809\ud1a0\ub9ac \uc0dd\uc131\n<ul class=\"wp-block-list\">\n<li>\ub514\ub809\ud1a0\ub9ac \uc774\ub984: <code>msa<\/code><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\uacb0\uacfc \ud655\uc778: <code>msa<\/code> \ub514\ub809\ud1a0\ub9ac \uc0dd\uc131<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">\uc720\uc804\uc790\uc758 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4 \ud68d\ub4dd<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uc778\uac04 amylase \ub2e8\ubc31\uc9c8\uc758 \uc11c\uc5f4 \uc815\ubcf4\ub97c \ud655\uc778\ud55c\ub2e4.<\/li>\n\n\n\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protein\/178585\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/www.ncbi.nlm.nih.gov\/protein\/178585<\/a><\/li>\n\n\n\n<li>FASTA format \ud615\uc2dd\uc758 \uc11c\uc5f4\uc744 \ubcf5\uc0ac\ud55c\ub2e4.<\/li>\n\n\n\n<li><code>msa\/amylase.fasta<\/code> \ud30c\uc77c\uc744 \uc0dd\uc131\ud558\uace0, \ubcf5\uc0ac\ud55c \ub0b4\uc6a9\uc744 \ubd99\uc5ec \ub123\uace0 \uc800\uc7a5\ud55c\ub2e4.<\/li>\n\n\n\n<li>\uacb0\uacfc \ud655\uc778: <code>msa\/amylase.fasta<\/code> \ud30c\uc77c \uc0dd\uc131<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">\uc9c4\ud654\uc801\uc73c\ub85c \uc5f0\uad00\ub41c \ub2e8\ubc31\uc9c8 \uc11c\uc5f4 \uc815\ubcf4 \ud68d\ub4dd<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>NCBI \ub370\uc774\ud130\ubca0\uc774\uc2a4\uc5d0\uc11c amylase\uc640 \uc9c4\ud654\uc801\uc73c\ub85c \uad00\ub828\ub41c \uc11c\uc5f4\uc744 \uc218\uc9d1\ud55c\ub2e4.\n<ul class=\"wp-block-list\">\n<li>URL: <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>BLAST\ub97c \uc774\uc6a9\ud558\uc5ec \uc720\uc0ac \uc11c\uc5f4 \uac80\uc0c9\n<ul class=\"wp-block-list\">\n<li>Protein BLAST \uc120\ud0dd<\/li>\n\n\n\n<li>FASTA format \uc11c\uc5f4 \uc785\ub825<\/li>\n\n\n\n<li>Database: Reference proteins (refseq_protein) \uc120\ud0dd<\/li>\n\n\n\n<li>\u2018BLAST\u2019 \ubc84\ud2bc \uc120\ud0dd<\/li>\n\n\n\n<li>\uc218 \ubd84 \uc18c\uc694<\/li>\n\n\n\n<li>\uacb0\uacfc \ud655\uc778<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\uc2e4\uc2b5\uc5d0 \uc0ac\uc6a9\ud560 \uc0c1\ub3d9 \uc720\uc804\uc790\uc758 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4 \uc120\ud0dd \ubc0f \ub2e4\uc6b4\ub85c\ub4dc\n<ul class=\"wp-block-list\">\n<li>MSA \uacb0\uacfc \uc2dc\uac01\ud654\uc758 \ud3b8\uc758\ub97c \uc704\ud574 5-10\uac1c\uc758 \uc11c\uc5f4\ub9cc \uc120\ud0dd<\/li>\n\n\n\n<li>&#8220;select all&#8221; \uc120\ud0dd\uc744 \ud574\uc81c\ud55c \ud6c4 \uac1c\ubcc4 \uc120\ud0dd<\/li>\n\n\n\n<li>\uc11c\ub85c \ub2e4\ub978 sequence identity (Per. ident) \uac12\uc744 \uac00\uc9c0\ub294 \uc11c\uc5f4 \uc120\ud0dd<\/li>\n\n\n\n<li>&#8220;Download&#8221; \ubc84\ud2bc \ud074\ub9ad\n<ul class=\"wp-block-list\">\n<li>&#8220;fasta(cluster)&#8221; \uc120\ud0dd \ud639\uc740 &#8220;fasta(aligned clusters)&#8221; \uc120\ud0dd<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\ub2e4\uc6b4\ub85c\ub4dc \uacbd\ub85c\ub97c \uae30\ub85d<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\ub2e4\uc6b4\ub85c\ub4dc \ud30c\uc77c \ubcf5\uc0ac\n<ul class=\"wp-block-list\">\n<li>\ub2e4\uc6b4\ub85c\ub4dc \ud30c\uc77c\uc744 <code>msa<\/code> \ub514\ub809\ud1a0\ub9ac\ub85c \ubcf5\uc0ac<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\uacb0\uacfc \ud655\uc778: <code>msa\/seqdump.txt<\/code> \ud30c\uc77c \uc0dd\uc131<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Query \uc11c\uc5f4 \ucd94\uac00<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Query \uc11c\uc5f4\uc744 \ub2e4\uc6b4\ub85c\ub4dc\ud55c sequence \ud30c\uc77c\uc5d0 \ucd94\uac00\ud55c\ub2e4.<\/li>\n\n\n\n<li><code>msa\/seqdump.txt<\/code> \ud30c\uc77c\uc758 \uac00\uc7a5 \uc0c1\ub2e8\uc5d0, <code>msa\/amylase.fasta<\/code> \ud30c\uc77c\uc758 \uc11c\uc5f4\uc744 \ucd94\uac00\ud55c\ub2e4.<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Multiple sequence alignment using Clustal Omega<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Multiple sequence alignment\ub97c \uc218\ud589\ud55c\ub2e4.<\/li>\n\n\n\n<li><code>msa\/msa.ipynb<\/code> \ub178\ud2b8\ubd81 \uc0dd\uc131<\/li>\n\n\n\n<li>\uc544\ub798 \uba85\ub839\uc744 code cel\uc5d0 \uc785\ub825\ud558\uace0 \uc2e4\ud589<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">!clustalo -i seqdump.txt -o amylase_aln.txt\n<\/code><\/pre>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uacb0\uacfc \ud655\uc778: <code>msa\/amylase_aln.txt<\/code> \ud30c\uc77c \uc0dd\uc131<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Multiple sequence alignment \uacb0\uacfc \ud655\uc778<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">MSA \uacb0\uacfc \ud655\uc778<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uc544\ub798 \ucf54\ub4dc\ub97c \uc774\uc6a9\ud558\uc5ec MSA \uacb0\uacfc\ub97c \ud655\uc778\ud55c\ub2e4.<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">from Bio import AlignIO\n\nalignment = AlignIO.read(open(\"amylase_aln.txt\"), \"fasta\")\nprint(\"Alignment length %i\" % alignment.get_alignment_length())\n\nfor record in alignment:\n\tprint(record.seq + \" \" + record.id)\n<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\ubcf4\uc874 \uc601\uc5ed \ubc0f \uac00\ubcc0 \uc601\uc5ed \ud0d0\uc0c9<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uac01 \uc704\uce58(position)\uc5d0\uc11c \uc544\ubbf8\ub178\uc0b0\uc758 \ubd84\ud3ec\ub97c \uacc4\uc0b0\ud55c\ub2e4.<\/li>\n\n\n\n<li>\uc774\ub97c \ud1b5\ud574 \ubcf4\uc874\ub41c \uc601\uc5ed\uacfc \ubcc0\uc774\uac00 \ub9ce\uc740 \uc601\uc5ed\uc744 \ud30c\uc545\ud55c\ub2e4.<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">m = len(alignment)\nn = len(alignment[0].seq)\n\nrecords = []\nfor i in range(n):\n    cnt = {}\n    for j in range(m):\n        c = alignment[j].seq[i]\n        if c not in cnt:\n            cnt[c] = 1\n        else:\n            cnt[c] += 1\n    records.append(cnt)\n    print(i+1, ' '.join(['%s:%d'%(c, cnt[c]) for c in cnt]))       \n<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\uac00\ubcc0 \uc601\uc5ed \uc2dc\uac01\ud654<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\uac01 \uc704\uce58\uc5d0\uc11c \uad00\ucc30\ub418\ub294 \uc11c\ub85c \ub2e4\ub978 \uc544\ubbf8\ub178\uc0b0\uc758 \uac1c\uc218\ub97c \uc2dc\uac01\ud654\ud55c\ub2e4.<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\"># Count alphabets at each position\nimport seaborn as sns\nimport matplotlib.pyplot as plt\n\ncs = [len(e) for e in records]\n\nsns.lineplot(x=range(len(cs)), y=cs)\nplt.xlabel(\"Position\")\nplt.ylabel(\"Number of amino acids\")\nplt.show()\n<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\uc0dd\uac01\ud574\ubcfc \ubb38\uc81c<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>\ub2e4\uc591\ud55c \uc544\ubbf8\ub178\uc0b0\uc774 \uc874\uc7ac\ud558\ub294 \uc704\uce58\uac00 \uc788\ub294\uc9c0 \ud655\uc778\ud558\ub77c.<\/li>\n\n\n\n<li>\ud574\ub2f9 \uc704\uce58\uc5d0\uc11c \ubc1c\uacac\ub418\ub294 \uc544\ubbf8\ub178\uc0b0\ub4e4\uc758 \ubb3c\ub9ac\ud654\ud559\uc801 \uc131\uc9c8(\uc608: \uadf9\uc131, \uc804\ud558, \ud06c\uae30)\uc744 \ube44\uad50\ud558\ub77c.<\/li>\n\n\n\n<li>\uc131\uc9c8\uc774 \uc720\uc0ac\ud558\ub2e4\uba74 \uadf8 \uc774\uc720\ub97c \uc124\uba85\ud558\ub77c.<\/li>\n\n\n\n<li>\uc131\uc9c8\uc774 \uc11c\ub85c \ub2e4\ub978 \uc544\ubbf8\ub178\uc0b0\uc774 \uc874\uc7ac\ud55c\ub2e4\uba74 \uadf8 \uc774\uc720\ub97c \uc124\uba85\ud558\ub77c.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Introduction \ubcf8 \uc2e4\uc2b5\uc5d0\uc11c\ub294 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4\uc744 \uc218\uc9d1\ud558\uace0, Multiple Sequence Alignment (MSA)\ub97c \uc218\ud589\ud558\uc5ec\uc11c\uc5f4 \uac04\uc758 \ubcf4\uc874 \uc601\uc5ed(conserved region)\uacfc \uac00\ubcc0 \uc601\uc5ed(variable region)\uc744 \ubd84\uc11d\ud55c\ub2e4. Multiple sequence alignment \uc218\ud589 \uc2e4\uc2b5 \ub514\ub809\ud1a0\ub9ac \uad6c\uc131 \uc720\uc804\uc790\uc758 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4 \ud68d\ub4dd \uc9c4\ud654\uc801\uc73c\ub85c \uc5f0\uad00\ub41c \ub2e8\ubc31\uc9c8 \uc11c\uc5f4 \uc815\ubcf4 \ud68d\ub4dd Query \uc11c\uc5f4 \ucd94\uac00 Multiple sequence alignment using Clustal Omega Multiple sequence alignment \uacb0\uacfc \ud655\uc778 MSA \uacb0\uacfc \ud655\uc778 \ubcf4\uc874 \uc601\uc5ed [&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":"set","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":[33,21],"tags":[],"class_list":["post-4632","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","category-classes"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Activity for Multiple Sequence Alignment - Biomedical Data Science Laboratory<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/activity-multiple-sequence-alignment\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Activity for Multiple Sequence Alignment - Biomedical Data Science Laboratory\" \/>\n<meta property=\"og:description\" content=\"Introduction \ubcf8 \uc2e4\uc2b5\uc5d0\uc11c\ub294 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4\uc744 \uc218\uc9d1\ud558\uace0, Multiple Sequence Alignment (MSA)\ub97c \uc218\ud589\ud558\uc5ec\uc11c\uc5f4 \uac04\uc758 \ubcf4\uc874 \uc601\uc5ed(conserved region)\uacfc \uac00\ubcc0 \uc601\uc5ed(variable region)\uc744 \ubd84\uc11d\ud55c\ub2e4. Multiple sequence alignment \uc218\ud589 \uc2e4\uc2b5 \ub514\ub809\ud1a0\ub9ac \uad6c\uc131 \uc720\uc804\uc790\uc758 \ub2e8\ubc31\uc9c8 \uc11c\uc5f4 \ud68d\ub4dd \uc9c4\ud654\uc801\uc73c\ub85c \uc5f0\uad00\ub41c \ub2e8\ubc31\uc9c8 \uc11c\uc5f4 \uc815\ubcf4 \ud68d\ub4dd Query \uc11c\uc5f4 \ucd94\uac00 Multiple sequence alignment using Clustal Omega Multiple sequence alignment \uacb0\uacfc \ud655\uc778 MSA \uacb0\uacfc \ud655\uc778 \ubcf4\uc874 \uc601\uc5ed [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/activity-multiple-sequence-alignment\/\" \/>\n<meta property=\"og:site_name\" content=\"Biomedical Data Science Laboratory\" \/>\n<meta property=\"article:published_time\" content=\"2026-04-15T00:52:41+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2026-04-15T00:57:36+00:00\" \/>\n<meta name=\"author\" content=\"sphong\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"sphong\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/activity-multiple-sequence-alignment\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/activity-multiple-sequence-alignment\\\/\"},\"author\":{\"name\":\"sphong\",\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/#\\\/schema\\\/person\\\/8d22f775fcc218b1184ec0d890034e9b\"},\"headline\":\"Activity for Multiple Sequence Alignment\",\"datePublished\":\"2026-04-15T00:52:41+00:00\",\"dateModified\":\"2026-04-15T00:57:36+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/activity-multiple-sequence-alignment\\\/\"},\"wordCount\":83,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/#organization\"},\"articleSection\":[\"Bioinformatics\",\"Classes\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/activity-multiple-sequence-alignment\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/activity-multiple-sequence-alignment\\\/\",\"url\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/activity-multiple-sequence-alignment\\\/\",\"name\":\"Activity for Multiple Sequence Alignment - 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