{"id":8818,"date":"2025-05-05T09:26:52","date_gmt":"2025-05-05T00:26:52","guid":{"rendered":"http:\/\/dna.brc.riken.jp\/en\/?page_id=8818"},"modified":"2025-05-05T09:27:34","modified_gmt":"2025-05-05T00:27:34","slug":"bacbrowser01en","status":"publish","type":"page","link":"http:\/\/dna.brc.riken.jp\/en\/bacyacen\/bacbrowser01en","title":{"rendered":"Searching BAC clone by the BAC browser"},"content":{"rendered":"<p><!-- js calling begin --><code><script type=\"text\/javascript\" src=\"\/en\/wp-content\/uploads\/js\/functions_list.js\"><\/script><\/code><!-- js calling end --><br \/>\nThe BAC browser is a tool to support identifications of clones within a given genomic regions based on the BAC end sequences. The search box at the page head allows you to enter a term, such as a gene symbol, Entrez GeneID, BAC end DDBJ ID and so on.<\/p>\n<h4>BAC Browsers<\/h4>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/teikyo01_green.gif\" alt=\"teikyo01_green\" width=\"30\" height=\"30\" \/><a href=\"http:\/\/analysis2.lab.nig.ac.jp\/mouseBrowser\/cgi-bin\/index.cgi?org=mm\">Mouse BAC browser (C57BL\/6N and MSM\/Ms)<\/a><br \/>\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/teikyo01_green.gif\" alt=\"teikyo01_green\" width=\"30\" height=\"30\" \/><a href=\"http:\/\/analysis2.lab.nig.ac.jp\/ratBrowser\/cgi-bin\/index.cgi?org=rn\">Rat BAC browser (F344\/Stm and LE\/Stm)<\/a><br \/>\n<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/teikyo01_green.gif\" alt=\"teikyo01_green\" width=\"30\" height=\"30\" \/><a href=\"http:\/\/analysis2.lab.nig.ac.jp\/jmonkeyBrowser\/cgi-bin\/index.cgi?org=jm\">Japanese macaque BAC browser (M. fuscata)<\/a><\/p>\n<h4>Clone search<\/h4>\n<ol>\n<li>Set search field (red square in the Fig. 1) to &#8220;Ncbi symbol&#8221;, for example, enter a gene symbol and click submit button.<br \/>\n<img loading=\"lazy\" decoding=\"async\" class=\"aligncenter\" src=\"https:\/\/dnaconda.riken.jp\/images\/bacbrowser_01.png\" alt=\"bacbrws01\" width=\"500\" height=\"326\" \/><\/p>\n<p style=\"text-align: center;\">Fig. 1 Mouse BAC browser.<\/p>\n<\/li>\n<li>The results of a symbol search is indicated as a tabular summary of markers that contained your search term, chromosome and location on which those markers are found. Click &#8220;jump to map&#8221; (red square in the Fig. 2) of an appropriate gene in the table to move Map View. Please set your browser allowing pop-up windows.<br \/>\n<img loading=\"lazy\" decoding=\"async\" class=\"aligncenter\" src=\"https:\/\/dnaconda.riken.jp\/images\/bacbrowser_02.png\" alt=\"bacclonebrowser2\" width=\"600\" height=\"87\" \/><\/p>\n<p style=\"text-align: center;\">Fig. 2. Tabular summary of search results.<\/p>\n<\/li>\n<li>The top of the Map View shows the chromosome number and center position of the view. The query (gene symbol) are appeared in the &#8220;NCBI field&#8221; with orange marker (red square A in the Fig. 3).<br \/>\nBAC clones having two-mapped ends are indicated as blue line (ex. B6Ng01-280P15) as in the green square B in Fig. 3. BAC end indicated as boxes (see yellow triangle<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/bacbrowser_04.png\" alt=\"\" width=\"14\" height=\"20\" \/>) are analyzed. Click Clone ID to see the BAC end sequence.<br \/>\nHowever, those with single-mapped end are indicated as red line (ex. B6Ng01-240E03) and unanalyzed end has no box (see red triangle<img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/bacbrowser_05.png\" alt=\"\" width=\"14\" height=\"20\" \/>). Please note that the length of red line doesn&#8217;t reflect actual size of the insert but an average length of insert of the BAC library.<br \/>\n<img loading=\"lazy\" decoding=\"async\" class=\"aligncenter\" src=\"https:\/\/dnaconda.riken.jp\/images\/bacbrowser_03.png\" alt=\"bacclonebrowser3\" width=\"650\" height=\"642\" \/><\/p>\n<p style=\"text-align: center;\">Fig. 3. Map View of BAC browser.<\/p>\n<\/li>\n<\/ol>\n<p style=\"text-align: left;\">2025.05.05 (N.N. GRP0002e)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The BAC browser is a tool to support identifications of clones within a given genomic regions based on the BAC end sequences. The search box at the page head allows you to enter a term, such as a gene symbol, Entrez GeneID, BAC end DDBJ ID and so on. BAC Browsers Mouse BAC browser (C57BL\/6N and MSM\/Ms) Rat BAC browser (F344\/Stm and LE\/Stm) Japanese macaque BAC browser (M. fuscata) Clone search Set search field (red square in the Fig. 1) to &#8220;Ncbi symbol&#8221;, for example, enter a gene symbol and click submit button. Fig. 1 Mouse BAC browser. The results of a symbol search is indicated as a tabular summary of markers that contained your search term, chromosome and location on which those markers are found. Click &#8220;jump to map&#8221; (red square in the Fig. 2) of an appropriate gene in the table to move Map View. Please set your browser allowing pop-up windows. Fig. 2. Tabular summary of search results. The top of the Map View shows the chromosome number and center position of the view. The query (gene symbol) are appeared in the &#8220;NCBI field&#8221; with orange marker (red square A in the Fig. 3). BAC clones having [&hellip;]<\/p>\n","protected":false},"author":13,"featured_media":0,"parent":8803,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","_seopress_robots_follow":"","_seopress_robots_imageindex":"","_seopress_robots_snippet":"","_seopress_robots_primary_cat":"","_seopress_robots_breadcrumbs":"","_seopress_robots_freeze_modified_date":"","_seopress_robots_custom_modified_date":"","_seopress_robots_canonical":"","_seopress_social_fb_title":"","_seopress_social_fb_desc":"","_seopress_social_fb_img":"","_seopress_social_fb_img_attachment_id":0,"_seopress_social_fb_img_width":0,"_seopress_social_fb_img_height":0,"_seopress_social_twitter_title":"","_seopress_social_twitter_desc":"","_seopress_social_twitter_img":"","_seopress_social_twitter_img_attachment_id":0,"_seopress_social_twitter_img_width":0,"_seopress_social_twitter_img_height":0,"_seopress_redirections_value":"","_seopress_redirections_enabled":"","_seopress_redirections_enabled_regex":"","_seopress_redirections_logged_status":"both","_seopress_redirections_param":"","_seopress_redirections_type":301,"_seopress_analysis_target_kw":"","footnotes":"","_wp_rev_ctl_limit":""},"class_list":["post-8818","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8818","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/comments?post=8818"}],"version-history":[{"count":2,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8818\/revisions"}],"predecessor-version":[{"id":8822,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8818\/revisions\/8822"}],"up":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8803"}],"wp:attachment":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/media?parent=8818"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}