Main features of the GenDB system
The development of the genome annotation system GenDB started in 1999 when the first whole genome sequencing projects were initiated by the chair of genetics at Bielefeld University. Over the past years the system has been continuously adapted to changing requirements and numerous new features were implemented to support microbial genome projects in the best possible way. Recently, we have extended the data model of the system and developed the necessary analysis and visualization tools to handle eukaryotic genomes as well. Some of the main features of the GenDB genome annotation platform are briefly listed below:
- web-based interface to allow users from all over the world to access a GenDB installation
- flexible configuration system for customizing analysis
- support for various gene prediction tools (Critica, Glimmer, Prodigal, Gismo) and as well for other kind of regions (tRNAScan, RNAMMER, TransTerm etc.)
- BLAST, HMMER 2/3, InterProScan and various other tools for function prediction
- automated pipeline to process from raw contig to fully functional annotated genome
- emphasis on both manual and automatic annotation
- visualization and browsing of genome using various classification schemes, e.g. EC number and COG functional categories
- role-based access management
- complete automated processing of an E.coli sized genome within a day
- ability to interact with other software developed in our group, e.g. EDGAR
GenDB has already been used in the annotation of over 60 bacterial genomes. Support for eukaryotic genomes is available on request based on the GenDBe platform that was recently developed for analyzing the genomes of the Chinese Hamster, sugar beet and other crop plants.
The following pages illustrate the main features of the GenDB software platform.