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

By Folker Meyer, Alexander Goesmann, Alice Carolyn McHardy, D. Bartels, T. Bekel, Jörn Clausen, Jörn Kalinowski, Burkhard Linke, O. Rupp, Robert Giegerich and 1 more. Nucleic Acids Research, 2003

721 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/2862b3065bcae300d6071470f5b3c80e7f45b5f9

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Citations in the corpus

Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021 (2013, positive): “Newly identifed sRNAs were named following the scheme SMx_sRNA_x and added to the S. meliloti GenDB database [39].”
Ecology of marine Bacteroidetes: a comparative genomics approach (2013, methodology): “2 (Meyer et al., 2003), supplemented by the tool JCoast (Richter et al., 2008).”
The RAST Server: Rapid Annotations using Subsystems Technology (2008, background): “This has led to the obvious conclusion that most of the annotations that will be associated with these newly-sequenced genomes will be provided through technologies that are largely automated, and a growing number of efforts focusing on different aspects of automated annotation have emerged [1-6].”
High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa (2020, methodology): “Predicted genes were functionally annotated using a modified version of the genome annotation platform GenDB 2.0 (Meyer 2003) for eukaryotic genomes as previously described (Rupp et al.”
Handbook of Corynebacterium glutamicum (2005, methodology): “The plot was generated by GenDB version 2.0 [27].”
MaGe: a microbial genome annotation system supported by synteny results (2006, methodology): “Examples of commonly used annotation platforms are given by commercial systems, such as ERGO (7) or Pedant-Pro (successor of PEDANT), and open source systems, such as Artemis (8), GenDB (9) or Manatee (TIGR, unpublished).”
BASys: a web server for automated bacterial genome annotation (2005, methodology): “genome annotation tools have been created, Gene-Quiz (1), PEDANT (3), MAGPIE/BLUEJAY (4,5), GenDB ( 6 ) and the TIGR CMR (7).”
EDGAR: A software framework for the comparative analysis of prokaryotic genomes (2009, methodology): “Furthermore, the integration between EDGAR and the automatic annotation framework GenDB [14] will be expanded by integrating direct links from EDGAR to GenDB annotations.”