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PMID: 12682369 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

GenDB--an open source genome annotation system for prokaryote genomes.

Nucleic acids research ·Vol. 31 ·No. 8 ·2003-04-15 ·Pages 2187-95

Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A

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.

MeSH Terms
Amino Acid Sequence Bacteria/genetics Base Sequence Computational Biology/methods Genome Genome, Bacterial Internet Molecular Sequence Data Prokaryotic Cells/metabolism Sequence Homology, Amino Acid Software
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Meyer Folker
Center for Genome Research, Department of Biology, Bielefeld University, Bielefeld, Germany. fm@genetik.uni-bielefeld.de
Goesmann Alexander
McHardy Alice C
Bartels Daniela
Bekel Thomas
Clausen Jörn
Kalinowski Jörn
Linke Burkhard
Rupp Oliver
Giegerich Robert
Pühler Alfred
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkg312
Email
fm@genetik.uni-bielefeld.de
Published
2003-04-15
Pages
2187-95
Language
English
Region
England
NLM ID
0411011
PMCID
PMC153740
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkg312 PMC Full Text View journal details
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