Rice instance of daTALbase: http://bioinfo-web.mpl.ird.fr/cgi-bin2/datalbase/index.cgi
daTALbase is a curated relational database that integrates TALE-related data including:
- bacterial TALE sequences
- plant promoter sequences
- predicted TALE binding sites
- transcriptomic data of host plants in response to TALE-harboring bacteria
- and other associated data.
The database can be explored to uncover candidate new susceptibility genes, as well as to study variation in TALE repertories and their corresponding targets.
Screenshot of daTALbase instance of Rice.
1- Git clone
git clone https://github.com/SouthGreenPlatform/daTALbase.git
cd daTALbase
2- Create and populate your database
Go to database directory and connect to your mysql server
cd database
mysql -u MYLOGIN -h MYHOST -p
Create the schema
mysql> create database MYDATABASENAME;
mysql> use MYDATABASENAME;
mysql>\. daTALbase_schema.sql
Using the templates_files as examples, you will be able to populate the database as follows:
mysql>LOAD DATA LOCAL INFILE 'PATH_TO_FILES/bacteria.txt' INTO TABLE bacteria;
3- Copy directories into dedicated HTML and CGI directories
mkdir <DATALBASE_HTML_DIR>
cd <DATALBASE_PATH>/html
cp * <DATALBASE_HTML_DIR>
mkdir <DATALBASE_CGI_BIN_DIR>
cd <DATALBASE_PATH>/cgi-bin
cp * <DATALBASE_CGI_BIN_DIR>
4- Edit the Configuration file and javascript
cd <DATALBASE_CGI_BIN_DIR>/Config
vi Configuration.pm
Edit the variable "url" (which is called several times) in javascript file
cd <DATALBASE_HTML_DIR>/javascript
vi functions.js
5- Access to your database using the URL defined by the variable $CGI_WEB_DIR in Configuration.pm
$CGI_WEB_DIR/index.cgi