{"id":390,"date":"2006-11-17T13:35:24","date_gmt":"2006-11-17T11:35:24","guid":{"rendered":"http:\/\/www.wjst.de\/blog\/papers\/supplements\/2004bmcbioinformaticssuppl\/"},"modified":"2018-10-25T06:17:22","modified_gmt":"2018-10-25T05:17:22","slug":"2004bmcbioinformaticssuppl","status":"publish","type":"page","link":"https:\/\/www.wjst.de\/blog\/papers\/supplements\/2004bmcbioinformaticssuppl\/","title":{"rendered":"2004BMCBioinformaticsSuppl"},"content":{"rendered":"
\n

BMC Bioinformatics 2004 Jul 12;5(1):92<\/h3>\n

The annotation pipeline has been run on 396 genes in the human chromosome 6p21.<\/p>\n

Data<\/h3>\n

Here are the SQL statements<\/a> to rebuild a database in SQL Server 2000 and an ASCII text file<\/a> with all SNPs for import into the database.<\/p>\n

To run the scripts you will need a freeware version of SQL Server<\/a>
\nand a cold fusion engine<\/a>. You will also need the
\nJava runtime engine<\/a>.<\/p>\n

Scripts<\/h3>\n

These cold fusion scripts will do all the annotation described in the paper:<\/p>\n

get SNP set: grab_snpper.cfm<\/a>
\nget sequence: grab_goldenpath.cfm<\/a>
\nget SNPs info: grab_dbsnp.cfm<\/a>
\nget TF annotation: grab_transfac.cfm<\/a>
\ndo man\/mouse alignment: grab_align.cfm<\/a>
\ndo cpg search: grab_cpg.cfm<\/a>
\ndo promoter search: grab_prom.cfm<\/a>
\nmerge and prepare view: graph.cfm<\/a>
\nrun annotation: grab_me.cmd<\/a><\/p>\n\n

 <\/p>\n

\n CC-BY-NC Science Surf , accessed 09.06.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"

BMC Bioinformatics 2004 Jul 12;5(1):92 The annotation pipeline has been run on 396 genes in the human chromosome 6p21. Data Here are the SQL statements to rebuild a database in SQL Server 2000 and an ASCII text file with all SNPs for import into the database. To run the scripts you will need a freeware … Continue reading 2004BMCBioinformaticsSuppl<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":338,"menu_order":4,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-390","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/pages\/390","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=390"}],"version-history":[{"count":1,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/pages\/390\/revisions"}],"predecessor-version":[{"id":10631,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/pages\/390\/revisions\/10631"}],"up":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/pages\/338"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=390"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}