2004BMCBioinformaticsSuppl

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 version of SQL Server
and a cold fusion engine. You will also need the
Java runtime engine.

Scripts

These cold fusion scripts will do all the annotation described in the paper:

get SNP set: grab_snpper.cfm
get sequence: grab_goldenpath.cfm
get SNPs info: grab_dbsnp.cfm
get TF annotation: grab_transfac.cfm
do man/mouse alignment: grab_align.cfm
do cpg search: grab_cpg.cfm
do promoter search: grab_prom.cfm
merge and prepare view: graph.cfm
run annotation: grab_me.cmd