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{"id":7239,"date":"2021-11-19T13:12:45","date_gmt":"2021-11-19T18:12:45","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=7239"},"modified":"2021-11-19T13:12:45","modified_gmt":"2021-11-19T18:12:45","slug":"expanded-genome-browsers-search","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/","title":{"rendered":"NCBI genome browsers: search and you will find!"},"content":{"rendered":"<p>If you’ve ever tried searching for a genomic location in NCBI’s <a class=\"external-link\" title=\"Follow link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/gdv\/?utm_source=blog&utm_medium=referral&utm_campaign=genome-browsers&utm_term=expanded-search&utm_content=20211119link1\" target=\"_blank\" rel=\"nofollow noopener\">Genome Data Viewer\u00a0<\/a>(GDV) or\u00a0<a class=\"external-link\" title=\"Follow link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/variation\/view?utm_source=blog&utm_medium=referral&utm_campaign=genome-browsers&utm_term=expanded-search&utm_content=20211119link2\" target=\"_blank\" rel=\"nofollow noopener\">Variation Viewer<\/a> and found that your search term didn’t work, it’s time to try again! We recently expanded support for searches in our genome browsers using non-NCBI identifiers such as <b>HGVS<\/b>\u00a0patterns (e.g.\u00a0NM_001318787.2:c.2258G>A) and\u00a0<b>Ensembl IDs<\/b>.\u00a0You can also search by\u00a0<b>chromosome coordinates<\/b>,\u00a0<b>cytogenetic band<\/b>,\u00a0<b>assembly scaffold<\/b>\/<b>component<\/b>,\u00a0<b>disease<\/b>\/<b>phenotype<\/b>,\u00a0<b>dbSNP identifier<\/b>, or\u00a0<b>RefSeq transcript<\/b>\/<b>protein accession<\/b>. We’ve gathered example searches in the table below.<\/p>\n<table class=\"confluenceTable\">\n<tbody>\n<tr>\n<th class=\"confluenceTh\" style=\"text-align: center;\">Search term<\/th>\n<th class=\"confluenceTh\" style=\"text-align: center;\">Example(s)<\/th>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">Chromosome coordinate<\/td>\n<td class=\"confluenceTd\">chr1:1,500,000-2,000,000<br \/>\nchr2: 1.5M-2,540.2K<br \/>\n3: 21.335M..21.337M<br \/>\n3: 21.335M..21.337M<br \/>\nchr5<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">Cytogenetic band<\/td>\n<td class=\"confluenceTd\">1p36.21<br \/>\n2q13<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">Assembly scaffold<\/td>\n<td class=\"confluenceTd\">NT_005403.18<br \/>\nNW_021159987.1<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">Assembly component<\/td>\n<td class=\"confluenceTd\">AC106865.4<br \/>\nAC018680.4<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">Gene\/protein name<\/td>\n<td class=\"confluenceTd\">PTEN<br \/>\nprotease<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">Disease\/phenotype<\/td>\n<td class=\"confluenceTd\">diabetes<br \/>\neye color<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">SNP rsID<\/td>\n<td class=\"confluenceTd\">rs863223352<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">dbVar ID<\/td>\n<td class=\"confluenceTd\">rs863223352<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">RefSeq transcript\/protein accession<\/td>\n<td class=\"confluenceTd\">NM_017551.3<br \/>\nXP_011538173.1<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">Ensembl gene\/transcript indentifier<\/td>\n<td class=\"confluenceTd\">ENSG00000233258<br \/>\nENST00000404547<\/td>\n<\/tr>\n<tr>\n<td class=\"confluenceTd\">HGVS<\/td>\n<td class=\"confluenceTd\">NM_001318787.2:c.2258G>A<br \/>\nNP_001289617: p.Arg272Cys<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>When you search by single coordinate, SNP or dbVar ID, or HGVS, the browser view zooms to the location of the search result. A marker is automatically created to identify the searched position.\u00a0 For HGVS, the marker is labelled with the corresponding rsID, if there is one.<\/p>\n<figure id=\"attachment_7242\" aria-describedby=\"caption-attachment-7242\" style=\"width: 1024px\" class=\"wp-caption alignnone\"><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/variation\/view?utm_source=blog&utm_medium=referral&utm_campaign=genome-browsers&utm_term=expanded-search&utm_content=20211119link2\" target=\"_blank\" rel=\"noopener\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"7242\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/variation-viewer-search-by-hgvs-results\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?fit=1898%2C782&ssl=1\" data-orig-size=\"1898,782\" 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=\"variation viewer search by HGVS results\" data-image-description=\"\" data-image-caption=\"<p>Figure 1. Variation Viewer showing results of search by an HGVS pattern, NP_001289617.1: p.Arg272Cys.<\/p>\n\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?fit=300%2C124&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?fit=1024%2C422&ssl=1\" class=\"size-large wp-image-7242\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?resize=1024%2C422&ssl=1\" alt=\"variation viewer search by HGVS results\" width=\"1024\" height=\"422\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?resize=1024%2C422&ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?resize=300%2C124&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?resize=150%2C62&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?resize=768%2C316&ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?resize=1536%2C633&ssl=1 1536w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?resize=1200%2C494&ssl=1 1200w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?resize=270%2C111&ssl=1 270w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?w=1898&ssl=1 1898w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/a><figcaption id=\"caption-attachment-7242\" class=\"wp-caption-text\"><strong>Figure 1.<\/strong> Variation Viewer showing results of search by an HGVS pattern, NP_001289617.1: p.Arg272Cys.<\/figcaption><\/figure>\n<p>As always, please contact us if you have additional questions or suggestions about this or any other feature in GDV or Variation Viewer. You can use\u00a0the\u00a0<a class=\"external-link\" title=\"Follow link\" href=\"https:\/\/www.research.net\/r\/F2T8XSC?a=GDV&from=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2F&p=landing&s=CE8D4393D80F9751_0914SID\" target=\"_blank\" rel=\"nofollow noopener\">Feedback<\/a>\u00a0button on the page or write to the NCBI\u00a0<a class=\"external-link\" title=\"Follow link\" href=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\" target=\"_blank\" rel=\"nofollow noopener\">Help Desk<\/a> directly.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>If you’ve ever tried searching for a genomic location in NCBI’s Genome Data Viewer\u00a0(GDV) or\u00a0Variation Viewer and found that your search term didn’t work, it’s time to try again! We recently expanded support for searches in our genome browsers using non-NCBI identifiers such as HGVS\u00a0patterns (e.g.\u00a0NM_001318787.2:c.2258G>A) and\u00a0Ensembl IDs.\u00a0You can also search by\u00a0chromosome coordinates,\u00a0cytogenetic band,\u00a0assembly scaffold\/component,\u00a0disease\/phenotype,\u00a0dbSNP … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">NCBI genome browsers: search and you will find!<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":0,"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":"NCBI genome browsers: search and you will find!","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":[33037050,5381386,574293891,10192294,651059058],"table_tags":[],"class_list":["post-7239","post","type-post","status-publish","format-standard","hentry","category-whats-new","tag-dbvar","tag-genome-browser","tag-genome-data-viewer","tag-dbsnp","tag-variation-viewer"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>NCBI genome browsers: search and you will find! - NCBI Insights<\/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:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"NCBI genome browsers: search and you will find! - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"If you’ve ever tried searching for a genomic location in NCBI’s Genome Data Viewer\u00a0(GDV) or\u00a0Variation Viewer and found that your search term didn’t work, it’s time to try again! We recently expanded support for searches in our genome browsers using non-NCBI identifiers such as HGVS\u00a0patterns (e.g.\u00a0NM_001318787.2:c.2258G>A) and\u00a0Ensembl IDs.\u00a0You can also search by\u00a0chromosome coordinates,\u00a0cytogenetic band,\u00a0assembly scaffold\/component,\u00a0disease\/phenotype,\u00a0dbSNP … Continue reading NCBI genome browsers: search and you will find! →\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/\" \/>\n<meta property=\"og:site_name\" content=\"NCBI Insights\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/ncbi.nlm\" \/>\n<meta property=\"article:published_time\" content=\"2021-11-19T18:12:45+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results-1024x422.png\" \/>\n<meta name=\"author\" content=\"NCBI Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@NCBI\" \/>\n<meta name=\"twitter:site\" content=\"@NCBI\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"NCBI Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"NCBI genome browsers: search and you will find!\",\"datePublished\":\"2021-11-19T18:12:45+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/\"},\"wordCount\":275,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results-1024x422.png\",\"keywords\":[\"Database of human genomic structural variation (dbVar)\",\"Genome Browser\",\"Genome Data Viewer (GDV)\",\"Single Nucleotide Polymorphism Database (dbSNP)\",\"Variation Viewer\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/\",\"name\":\"NCBI genome browsers: search and you will find! - NCBI Insights\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results-1024x422.png\",\"datePublished\":\"2021-11-19T18:12:45+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/11\/19\/expanded-genome-browsers-search\/#primaryimage\",\"url\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?fit=1898%2C782&ssl=1\",\"contentUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/11\/variation-viewer-search-by-HGVS-results.png?fit=1898%2C782&ssl=1\",\"width\":1898,\"height\":782,\"caption\":\"Figure 1. 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