UniGene DLST
UniGene DLST is a simple PHP/Apache/MySQL application that downloads and maintains local copies of UniGene genome tables. The default web site displays a list of genomes available in UniGene along with their most recent build number and date. If a genome has been downloaded, the build number and download date are also displayed.
When a user selects a genome, the gzipped data file is stored locally in a temporary file. The file is parsed into three linked MySQL tables. One table (data) contains one row for each UniGene cluster. A second table (sequence) contains one row for each GenBank Accession key in each cluster. The third table (express) stores gene expression data associated with each cluster. Once the downloaded flat file is parsed, the file is deleted.
Downloaded UniGene tables are useful for annotating microarrays or for comparing different microarrays from the same species through shared UniGene cluster numbers.
Comments:
- At this stage there is no administrative security--any user may download genomes. This will be changed in a future release.
- The OS user that is used by Apache must have write access to a folder for downloading files.
- Installation assumes that you have a server configured with Apache, PHP 4.X and MySQL.
Installation:
- Download the archive from the project page on Bioinformatics.org.
- Uncompress the archive (tar xzvf). Move it to a folder in the path of your web site. On MacOSX this is usually /Library/WebServer/Documents. On Linux this is usually /usr/local/www.
- If necessary, modify your httpd.conf file to establish the chosen location as a directory.
- Check that the "files" directory has write permission for the Apache username. The simplest and least secure method is to "chmod 777 files".
- Edit the unigene.class.inc file in the include folder. Class members (variables) that will require local editting are at the top of the file with commented instructions. Insert your email address, local MySQL server data, and full address of the local directory for writing files.
- Point a web browser to index.php.
(Click for screenshot)