title: GenDB--an open source genome annotation system for prokaryote genomes.
abstract: The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. To account for the individual needs of different projects, such a system should be modular and easily extensible. We present a genome annotation system for prokaryote genomes, which is well tested and readily adaptable to different tasks. The modular system was developed using an object-oriented approach, and it relies on a relational database backend. Using a well defined application programmers interface (API), the system can be linked easily to other systems. GenDB supports manual as well as automatic annotation strategies. The software currently is in use in more than a dozen microbial genome annotation projects. 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 open source.
authors.affiliation: Center for Genome Research, Department of Biology, Bielefeld University, Bielefeld, Germany. fm@genetik.uni-bielefeld.de
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Alice C
authors.initials: AC
authors.lastname: McHardy
authors.forename: Daniela
authors.initials: D
authors.lastname: Bartels
authors.forename: Thomas
authors.initials: T
authors.lastname: Bekel
authors.forename: Jörn
authors.initials: J
authors.lastname: Clausen
authors.forename: Jörn
authors.initials: J
authors.lastname: Kalinowski
authors.forename: Burkhard
authors.initials: B
authors.lastname: Linke
authors.forename: Oliver
authors.initials: O
authors.lastname: Rupp
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016678:Genome; D016680:Genome, Bacterial; D020407:Internet; D008969:Molecular Sequence Data; D011387:Prokaryotic Cells / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D012984:Software