The advent of new high throughput technologies opens the road towards a new era of genome analysis. Data from high throughput sequencers, chip based RNA expression analysis and proteome analysis systems create the need for software systems to support new kinds of analysis and data.

At the same time the focus of molecular research shifted from the analysis of single genes to the analysis of whole genomes, multiple high throughput sources of data are routinely used. Yet there is a shortage of software systems that help store, integrate and analyse the wealth of information now available.

We describe the development of a new genome annotation system (GENDB) based on a relational database system and object oriented technology that helps with the analysis of this data. GENDB significantly reduces the storage and compute overhead of existing systems, while offering more flexibility. The ability to integrate new kinds of data and new methods of analysis is one of the primary design targets for GENDB. The GENDB system has been succesfully used in a number of genome projects.