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GenDBE was developed based on the GenDB genome annotation system that was originally designed for prokaryotic genomes only. The system has been adapted to facilitate the creation and functional annotation of sequence features that are specific for eukaryotic genomes, e.g. intron and exon gene structures.

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The system has been developed as an extensible and user friendly framework for both bioinformatics researchers and biologists to use in their genome projects. The GenDBE annotation engine will automatically identify, classify and annotate genes using a large collection of software tools. Many groups view this automatic annotation as the first step that needs to be followed by expert annotation of the genome.

GenDBE offers user interfaces that allow expert annotation with large, geo-graphically dispersed teams of experts. Genes to be annotated can be categorized by functional class or gene location. A number of naming schemes (aka ontologies or functional classification schemes) are supported: EC numbers, GO, COG. In addition to its use as a production genome annotation system, it can be employed as a flexible framework for the large-scale evaluation of different annotation strategies. The software currently is in use several eukaryotic genome annotation projects.