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. 2003 Apr 15;31(8):2187-95.
doi: 10.1093/nar/gkg312.

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

Folker Meyer  1 , Alexander Goesmann, Alice C McHardy, Daniela Bartels, Thomas Bekel, Jörn Clausen, Jörn Kalinowski, Burkhard Linke, Oliver Rupp, Robert Giegerich, Alfred Pühler
Affiliations

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

Folker Meyer et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
The core data model of GenDB in UML. Only the three central classes are shown; the classes actually represent a hierarchy of specialized objects, e.g. a BLAST observation object and an InterPro observation object.
Figure 2
Figure 2
Overview of the GenDB system.
Figure 3
Figure 3
O2DBI maps Perl objects to relational tables, generating both SQL tables and Perl modules.
Figure 4
Figure 4
Main window of the GenDB system for navigation via the contig. A list in the left column allows the selection of a contig (here the pSymB megaplasmid of S.meliloti). The graphical overview in the top right window (RegionCanvas) displays the subregions of a selected contig (e.g. CDS, signal peptides, etc.) and computed observations of several gene predictors (here Glimmer and Critica). The RegionCanvas and the sequence browser at the bottom are synchronized. The window below the RegionCanvas contains information about the selected region or different plots (GC content, GC skew, etc.). The small contig overview in the middle can be used to display the positions of selected genes (here several genes of the metabolism of nucleotide sugars).
Figure 5
Figure 5
Visualization of a virtual 2D gel and navigation via a whole-genome representation. Highlighted spots and regions again show some genes of the metabolism of nucleotide sugars.
Figure 6
Figure 6
The observations, a single BLAST report and the underlying database record (via SRS) for a CDS region as shown by GenDB. The user can create a manual annotation by clicking on an observation.
Figure 7
Figure 7
Data navigation via KEGG pathways (here all annotated enzymes of the metabolism of nucleotide sugars for S.meliloti) or gene ontologies (here identified regions for a selected GO number).
Figure 8
Figure 8
A sample genome analysis pipeline implemented with GenDB.
See this image and copyright information in PMC

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