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GenDB is a genome annotation system for prokaryotic genomes. 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 GenDB 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.
GenDB 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 system is available as open source under the GNU public license (GPL). The modular system was developed using an object-oriented approach, and it relies on a relational database backend (e.g. MySQL). Using a well defined application programmers interface (API), the system can be linked easily to other systems. The software currently is in use in more than a dozen microbial genome annotation projects. Several partners/collaborators have installed GenDB and use it for in-house genome annotation.