Download xGDB !


The xGDB project provides scientists with an online portal for the integration of diverse sources of genomic data.

Portals allow researchers to effectively target a specific scientific question by customizing their interactions with available data. For instance, scientist interested in the location and structure of genes often need to verify the supporting evidence for said structure and location. This can be done by visually comparing the alignment of laboratory generated sequences known as ESTs (and their assembled cousin cDNA). Such comparison requires a system for integrating these types of data.

Projects such as the gmod project (hosted at sourceforge) allow for such comparisons on a general scale, yet are mostly intended for community wide database systems. The xGDB system provides a more personal lab or group centered environment which can be tailored by individual users to their specific needs.

The xGDB system provides this infrastructure using standard Perl and PHP CGI scripting, integration with an Apache (or other appropriate) web server and access to federated databases (remotely maintained or locally established).

Showcase xGDB instances can be browsed by following the links on the left.


In order to use the eXtensible Genome Data Broker you will need the following:

  1. A Relational Database Management System [ The MySQL RDMS is recommended ]
  2. A Webserver [ The Apache Webserver is recommended ]
  3. The PHP scripting webserver extension
  4. The Perl scripting language and execution environment
  5. The NCBI-BLAST application package


  • 15 July 2006

    The first official ditribution of xGDB has been packaged and is available here.

  • 10 July 2006

    Congrats to the yrGATE project. They've been published.

  • 15 Feb 2006

    The CVS repository of xGDB is now being frozen at a Beta-stable state every Friday (noon) to Monday (noon)

  • 3 Jan 2006

    The xGDB project site is now available at


  • xGDB core (v1)
  • Toolkit Integration (web-service extensions)
    • GAEVAL (v1): Genome Annotation Evaluation
    • yrGATE (v1): your Gene structure Annotation Tool for Eukaryotes
    • DAS client: Distributed Annotation Service
  • Feature Component Extensions (XGDB-FCM)
    • TIGR xml Gene Annotations
    • BioDBGFF Bioperl/GMOD GFF features