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{"id":11601,"date":"2023-06-08T11:01:00","date_gmt":"2023-06-08T15:01:00","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=11601"},"modified":"2023-06-08T11:01:00","modified_gmt":"2023-06-08T15:01:00","slug":"cgv-dot-plot","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/06\/08\/cgv-dot-plot\/","title":{"rendered":"New! The Comparative Genome Viewer (CGV) Dot Plot"},"content":{"rendered":"<h3><em>Get a High-Level View of Assembly-Assembly Alignments<\/em><\/h3>\n<p><span data-contrast=\"auto\">New feature! We added an alternate view in the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/cgv\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=cgv-dot-plot-20230608\"><span data-contrast=\"none\">Comparative Genome Viewer (CGV)<\/span><\/a><span data-contrast=\"auto\"> that shows a dot plot (also known as a 2D plot) comparing two related genome assemblies. This added view provides a high-level overview of the assembly-assembly alignment. Dot plots help you find large genome rearrangements such as translocations or segmental duplications more easily.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><\/p>\n<h5>Using the Dot Plot View<\/h5>\n<ol>\n<li data-leveltext=\"%1)\" data-font=\"Calibri\" data-listid=\"1\" data-list-defn-props=\"{"335552541":0,"335559684":-1,"335559685":720,"335559991":360,"469769242":[65533,0],"469777803":"left","469777804":"%1)","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span data-contrast=\"auto\">From the main CGV view, you can access the dot plot by clicking on the new \u2018Go to dot plot view\u2019 link. <\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"%1)\" data-font=\"Calibri\" data-listid=\"1\" data-list-defn-props=\"{"335552541":0,"335559684":-1,"335559685":720,"335559991":360,"469769242":[65533,0],"469777803":"left","469777804":"%1)","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span data-contrast=\"auto\">Click on a cell in the plot to zoom to a pairwise comparison between two chromosomes.\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"%1)\" data-font=\"Calibri\" data-listid=\"1\" data-list-defn-props=\"{"335552541":0,"335559684":-1,"335559685":720,"335559991":360,"469769242":[65533,0],"469777803":"left","469777804":"%1)","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span data-contrast=\"auto\">You can return to the main CGV view by clicking on \u2019Go to ideogram view\u2019.\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><\/li>\n<li data-leveltext=\"%1)\" data-font=\"Calibri\" data-listid=\"1\" data-list-defn-props=\"{"335552541":0,"335559684":-1,"335559685":720,"335559991":360,"469769242":[65533,0],"469777803":"left","469777804":"%1)","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span data-contrast=\"auto\">When you return to the ideogram view from the chromosome level dot plot view, you\u2019ll see the same chromosomes you were looking at in the dot plot. Here, you can zoom further to investigate gene annotation and obtain alignment details.\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":160,"335559740":259}\">\u00a0<\/span><\/li>\n<\/ol>\n<p><!--more--><\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"11604\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/06\/08\/cgv-dot-plot\/dotplot_cgv\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?fit=871%2C935&ssl=1\" data-orig-size=\"871,935\" data-comments-opened=\"1\" data-image-meta=\"{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}\" data-image-title=\"dotplot_CGV\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?fit=279%2C300&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?fit=871%2C935&ssl=1\" class=\"alignright size-full wp-image-11604\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?resize=871%2C935&ssl=1\" alt=\"\" width=\"871\" height=\"935\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?w=871&ssl=1 871w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?resize=279%2C300&ssl=1 279w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?resize=140%2C150&ssl=1 140w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?resize=768%2C824&ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/dotplot_CGV.png?resize=252%2C270&ssl=1 252w\" sizes=\"auto, (max-width: 871px) 100vw, 871px\" \/><\/p>\n<p><em><b>Figure 1:<\/b> An example of a <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/cgv\/plot\/GCF_011064425.1\/GCF_015227675.2\/16975\/10116?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=cgv-dot-plot-20230608\">dot plot<\/a> between assemblies for the Norway rat (<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCF_015227675.2\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=cgv-dot-plot-20230608\">mRatBN7.2<\/a>) and black rat (<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCF_011064425.1\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=cgv-dot-plot-20230608\">Rrattus_CSIRO_v1<\/a>). Norway rat chromosomes are plotted on the X axis. Black rat chromosomes are plotted on the Y axis. Dots or lines represent locations of assembly alignment; alignments in the same orientation are green, while those in the reverse orientation are graphed with an opposite slope and are colored purple.\u00a0<\/em><\/p>\n<h5>Learn more<\/h5>\n<p><span data-contrast=\"auto\">Learn how to use the CGV dot plot! For more information about CGV and for step-by-step instructions on how to use it, check out our <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/cgv\/cm\/cgv\/more_info?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=cgv-dot-plot-20230608#Dotplot_view\"><span data-contrast=\"none\">help documentation<\/span><\/a><span data-contrast=\"auto\">.\u00a0\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Stay up to date<\/h5>\n<p><span data-contrast=\"auto\">CGV is a part of the\u202f<\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/comparative-genomics-resource\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=cgv-dot-plot-20230608\"><span data-contrast=\"none\">NIH Comparative Genomics Resource (CGR)<\/span><\/a><span data-contrast=\"none\">. CGR facilitates reliable comparative genomics analyses\u202ffor all eukaryotic organisms through an NCBI Toolkit and community collaboration.\u202f\u202f\u202f<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">Follow us on Twitter\u202f<\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"none\">\u202fand\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_50%22\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"none\">\u202fto keep up to date with CGV and other CGR news.\u202f\u202f\u202f<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Questions?<\/h5>\n<p><span data-contrast=\"none\">If you have questions or would like to provide feedback, please reach out to us at <\/span><a href=\"mailto:info@ncbi.nlm.nih.gov\"><span data-contrast=\"none\">info@ncbi.nlm.nih.gov<\/span><\/a><span data-contrast=\"none\">.\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Get a High-Level View of Assembly-Assembly Alignments New feature! We added an alternate view in the Comparative Genome Viewer (CGV) that shows a dot plot (also known as a 2D plot) comparing two related genome assemblies. This added view provides a high-level overview of the assembly-assembly alignment. Dot plots help you find large genome rearrangements … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/06\/08\/cgv-dot-plot\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">New! The Comparative Genome Viewer (CGV) Dot Plot<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":11605,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"New! The Comparative Genome Viewer (CGV) Dot Plot","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[693060769],"table_tags":[],"class_list":["post-11601","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-comparative-genome-viewer-cgv"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>New! 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