{"id":2710,"date":"2021-12-28T14:33:45","date_gmt":"2021-12-28T14:33:45","guid":{"rendered":"https:\/\/cbirt.net\/staging\/?page_id=2710"},"modified":"2022-01-08T15:57:32","modified_gmt":"2022-01-08T15:57:32","slug":"sequence-analysis","status":"publish","type":"page","link":"https:\/\/cbirt.net\/staging\/sequence-analysis\/","title":{"rendered":"Sequence Analysis"},"content":{"rendered":"<p>[tdc_zone type=&#8221;tdc_content&#8221;][vc_row][vc_column][vc_empty_space][td_block_title title_tag=&#8221;h4&#8243; custom_title=&#8221;BIOINFORMATICS TOOLS&#8221; block_template_id=&#8221;&#8221; f_header_font_style=&#8221;italic&#8221; header_color=&#8221;#dd3333&#8243;][vc_row_inner][vc_column_inner width=&#8221;1\/4&#8243;][\/vc_column_inner][vc_column_inner width=&#8221;1\/2&#8243;][tdm_block_column_title title_text=&#8221;U2VxdWVuY2UlMjBBbmFseXNpcyUyMFRvb2xz&#8221; title_tag=&#8221;h3&#8243; title_size=&#8221;tdm-title-xsm&#8221; content_align_horizontal=&#8221;content-horiz-center&#8221; tds_title1-title_color=&#8221;eyJ0eXBlIjoiZ3JhZGllbnQiLCJjb2xvcjEiOiIjMDExYWE4IiwiY29sb3IyIjoiIzAxMWFhOCIsIm1peGVkQ29sb3JzIjpbXSwiZGVncmVlIjoiLTkwIiwiY3NzIjoiYmFja2dyb3VuZC1jb2xvcjogIzAxMWFhODsiLCJjc3NQYXJhbXMiOiIwZGVnLCMwMTFhYTgsIzAxMWFhOCJ9&#8243; tds_title=&#8221;tds_title2&#8243; el_class=&#8221;sequence-databases&#8221;][\/vc_column_inner][vc_column_inner width=&#8221;1\/4&#8243;][\/vc_column_inner][\/vc_row_inner][vc_row_inner][vc_column_inner width=&#8221;1\/4&#8243;][td_block_list_menu menu_id=&#8221;148&#8243; block_template_id=&#8221;td_block_template_18&#8243; menu_color=&#8221;#011aa8&#8243; menu_hover_color=&#8221;#dd3333&#8243; tdc_css=&#8221;eyJhbGwiOnsiYmFja2dyb3VuZC1jb2xvciI6IiNmZmZmZmYiLCJkaXNwbGF5IjoiIn19&#8243;][\/vc_column_inner][vc_column_inner width=&#8221;1\/2&#8243;][td_block_text_with_title tdc_css=&#8221;eyJhbGwiOnsiZGlzcGxheSI6IiJ9fQ==&#8221; block_template_id=&#8221;td_block_template_14&#8243; header_color=&#8221;#000000&#8243; el_class=&#8221;Nucleotide-Sequence-Databases&#8221; custom_title=&#8221;Pairwise Sequence Alignment&#8221;]<\/p>\n<ul>\n<li><a href=\"https:\/\/www.ebi.ac.uk\/Tools\/psa\/emboss_needle\/\" target=\"_blank\" rel=\"noopener\">Needle@EBI<\/a> &#8211; Needleman-Wunsch global sequence alignment tool.<\/li>\n<li><a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi\" target=\"_blank\" rel=\"noopener\">BLAST@NCBI<\/a> &#8211; Alignment tool to find regions of similarity between biological sequences.<\/li>\n<li><a href=\"https:\/\/www.rcsb.org\/alignment\" target=\"_blank\" rel=\"noopener\">Stucture Alignment<\/a> &#8211; Pairwise structure alignment tool at PDB.<\/li>\n<li><a href=\"https:\/\/www.ebi.ac.uk\/Tools\/psa\/emboss_water\/\" target=\"_blank\" rel=\"noopener\">Water@EBI<\/a> &#8211;\u00a0 For local sequence alignment based on Smith-Waterman algorithm.<\/li>\n<li><a href=\"https:\/\/dotlet.vital-it.ch\/\" target=\"_blank\" rel=\"noopener\">Dotlet@SIB<\/a> &#8211; Sequence comparison with dot plot.<\/li>\n<\/ul>\n<p>[\/td_block_text_with_title][td_block_text_with_title tdc_css=&#8221;eyJhbGwiOnsiZGlzcGxheSI6IiJ9fQ==&#8221; block_template_id=&#8221;td_block_template_14&#8243; header_color=&#8221;#000000&#8243; el_class=&#8221;Nucleotide-Sequence-Databases&#8221; custom_title=&#8221;Multiple Sequence Alignment&#8221;]<\/p>\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/tools\/cobalt\/\" target=\"_blank\" rel=\"noopener\">COBALT@NCBI<\/a> &#8211; Constraint-based Multiple Alignment Tool. Computes a multiple protein sequence alignment using conserved domain and local sequence similarity information.<\/li>\n<li><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/msa\/clustalo\" target=\"_blank\" rel=\"noopener\">Clustal Omega@EBI<\/a> &#8211; Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.<\/li>\n<li><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/msa\/muscle\/\" target=\"_blank\" rel=\"noopener\">Muscle@EBI<\/a> &#8211; MUltiple Sequence Comparison by Log- Expectation. Multiple sequence comparison with better average accuracy and speed.<\/li>\n<li><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/msa\/mafft\/\" target=\"_blank\" rel=\"noopener\">MAFFT@EBI<\/a> &#8211; Multiple Alignment using Fast Fourier Transform. High speed multiple sequence alignment program.<\/li>\n<li><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/msa\/kalign\/\" target=\"_blank\" rel=\"noopener\">KALIGN@EBI<\/a> &#8211; A fast and accurate multiple sequence alignment algorithm.<\/li>\n<li><a href=\"https:\/\/www.ebi.ac.uk\/Tools\/msa\/tcoffee\/\">T-Coffe@EBI<\/a> &#8211; Multiple alignment program that allows to combine results obtained with several alignment methods.<br \/>.<\/li>\n<li><a href=\"http:\/\/www.bioinformatics.org\/strap\/\" target=\"_blank\" rel=\"noopener\">STRAP<\/a> &#8211; Intuitive Editor for annotated multiple Sequence and Structure Alignments<\/li>\n<li><a href=\"http:\/\/weblogo.threeplusone.com\/\" target=\"_blank\" rel=\"noopener\">Weblogo<\/a> &#8211; A web based application designed to easily generate sequence logos .<\/li>\n<\/ul>\n<p>[\/td_block_text_with_title][td_block_text_with_title tdc_css=&#8221;eyJhbGwiOnsiZGlzcGxheSI6IiJ9fQ==&#8221; block_template_id=&#8221;td_block_template_14&#8243; header_color=&#8221;#000000&#8243; el_class=&#8221;Nucleotide-Sequence-Databases&#8221; custom_title=&#8221;Sequence Similarity Search&#8221;]<\/p>\n<ul>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/blast\/Blast.cgi\" target=\"_blank\" rel=\"noopener\">NCBI<\/a> &#8211;\u00a0Sequence similarity seacrh programs at NCBI including PSI-BLAST and PHI-BLAST, etc.<\/li>\n<li><a href=\"http:\/\/www.ebi.ac.uk\/Tools\/sss\/\" target=\"_blank\" rel=\"noopener\">EBI\u00a0<\/a> &#8211; Sequence similarity search programs at EBI\u00a0 including FASTA, BLAST and SSEARCH, GGSearch, GLSearch, HMMER.\u00a0<\/li>\n<li><a href=\"https:\/\/ensembl.org\/Multi\/Tools\/Blast\">BLAST\/BLAT@Ensembl<\/a> &#8211; Sequence similarity search tool at Ensembl.<\/li>\n<li><a href=\"http:\/\/genome.ucsc.edu\/cgi-bin\/hgBlat\">BLAT@UCSC<\/a> &#8211; Sequence similarity search program available at UCSC genome browser.<\/li>\n<li><a href=\"http:\/\/www.sanger.ac.uk\/DataSearch\/blast.shtml\" target=\"_blank\" rel=\"noopener\">Sanger BLAST<\/a> &#8211; Sanger Genome Sequencing Projects BLAST.<\/li>\n<\/ul>\n<p>[\/td_block_text_with_title][td_block_text_with_title tdc_css=&#8221;eyJhbGwiOnsiZGlzcGxheSI6IiJ9fQ==&#8221; block_template_id=&#8221;td_block_template_14&#8243; header_color=&#8221;#000000&#8243; el_class=&#8221;Nucleotide-Sequence-Databases&#8221; custom_title=&#8221;Primer Design&#8221;]<\/p>\n<ul>\n<li><a href=\"http:\/\/bioweb.uwlax.edu\/genweb\/molecular\/seq_anal\/primer_design\/primer_design.htm\" target=\"_blank\" rel=\"noopener\">Primer Design<\/a> &#8211; The online primer design tool at BioWeb.<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/tools\/primer-blast\/\" target=\"_blank\" rel=\"noopener\">Primer Blast<\/a> &#8211; NCBI primer design tool with Blast search.<\/li>\n<li><a href=\"http:\/\/www.yeastgenome.org\/cgi-bin\/web-primer\" target=\"_blank\" rel=\"noopener\">Web Primer<\/a> &#8211; Online primer design tool at the yeast genome database.<\/li>\n<\/ul>\n<p>[\/td_block_text_with_title][\/vc_column_inner][vc_column_inner width=&#8221;1\/4&#8243;][td_block_title title_tag=&#8221;h4&#8243; custom_title=&#8221;Must Read&#8221; block_template_id=&#8221;td_block_template_4&#8243; 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tds_title=&#8221;tds_title2&#8243; el_class=&#8221;sequence-databases&#8221;][\/vc_column_inner][vc_column_inner width=&#8221;1\/4&#8243;][\/vc_column_inner][\/vc_row_inner][vc_row_inner][vc_column_inner width=&#8221;1\/4&#8243;][td_block_list_menu menu_id=&#8221;148&#8243; block_template_id=&#8221;td_block_template_18&#8243; menu_color=&#8221;#011aa8&#8243; menu_hover_color=&#8221;#dd3333&#8243; tdc_css=&#8221;eyJhbGwiOnsiYmFja2dyb3VuZC1jb2xvciI6IiNmZmZmZmYiLCJkaXNwbGF5IjoiIn19&#8243;][\/vc_column_inner][vc_column_inner width=&#8221;1\/2&#8243;][td_block_text_with_title tdc_css=&#8221;eyJhbGwiOnsiZGlzcGxheSI6IiJ9fQ==&#8221; block_template_id=&#8221;td_block_template_14&#8243; header_color=&#8221;#000000&#8243; el_class=&#8221;Nucleotide-Sequence-Databases&#8221; custom_title=&#8221;Pairwise Sequence Alignment&#8221;] Needle@EBI &#8211; Needleman-Wunsch global sequence alignment tool. BLAST@NCBI &#8211; Alignment tool to find regions of similarity between biological sequences. Stucture Alignment &#8211; Pairwise&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_kad_post_transparent":"","_kad_post_title":"","_kad_post_layout":"","_kad_post_sidebar_id":"","_kad_post_content_style":"","_kad_post_vertical_padding":"","_kad_post_feature":"","_kad_post_feature_position":"","_kad_post_header":false,"_kad_post_footer":false,"_kad_post_classname":"","footnotes":""},"class_list":["post-2710","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v28.7 (Yoast SEO v28.7) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>Sequence Analysis - CBIRT<\/title>\n<meta name=\"description\" content=\"A curated list of top software&#039;s and tools used for analyzing sequences in Genomics, Proteomics, Bioinformatics and Computational Biology.\" \/>\n<meta name=\"robots\" content=\"noindex, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Sequence Analysis\" \/>\n<meta property=\"og:description\" content=\"A curated list of top software&#039;s and tools used for analyzing sequences in Genomics, Proteomics, Bioinformatics and Computational Biology.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/cbirt.net\/staging\/sequence-analysis\/\" \/>\n<meta property=\"og:site_name\" content=\"CBIRT\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/Centre.Bioinformatics.Research.Technology\" \/>\n<meta property=\"article:modified_time\" content=\"2022-01-08T15:57:32+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@CbirtDirector\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/cbirt.net\\\/staging\\\/sequence-analysis\\\/\",\"url\":\"https:\\\/\\\/cbirt.net\\\/staging\\\/sequence-analysis\\\/\",\"name\":\"Sequence Analysis - CBIRT\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/cbirt.net\\\/staging\\\/#website\"},\"datePublished\":\"2021-12-28T14:33:45+00:00\",\"dateModified\":\"2022-01-08T15:57:32+00:00\",\"description\":\"A curated list of top software's and tools used for analyzing sequences in Genomics, Proteomics, Bioinformatics and Computational Biology.\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/cbirt.net\\\/staging\\\/sequence-analysis\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/cbirt.net\\\/staging\\\/sequence-analysis\\\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/cbirt.net\\\/staging\\\/sequence-analysis\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/cbirt.net\\\/staging\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Sequence Analysis\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/cbirt.net\\\/staging\\\/#website\",\"url\":\"https:\\\/\\\/cbirt.net\\\/staging\\\/\",\"name\":\"CBIRT\",\"description\":\"Centre of Bioinformatics Research &amp; 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