GenDBWiki

GenDB Overview Page

GenDB - An open source genome annotation system for prokaryote genomes

The GenDB system is an open source genome annotation system developed by the "Bioinformatics Resource Facility (BRF)" of the "Center for Biotechnology (CeBiTec)" at "Bielefeld University".

Please have a look at the GenDB website for general information, a guided tour, login to a demo project, a list of FAQs and more information about the availability of this software. Within this GenDB Wiki you will find more detailed information about installing and maintaining GenDB, using the system, and writing your own programs. Since this information is likely to change quite frequently we decided to put it into a Wiki system. If you discover new features that are not listed here you are of course welcome to extend this documentation.

Since GenDB version 2.2 the sources are split into 3 separate major packages:

• GenDB CORE includes the complete GenDB backend with all O2DBI class modules and several extensions but no graphical user interface. It contains the basic functionality for annotating a genome automatically by using a number of simple scripts available within this package.
• GenDB WEB contains the modules required for running the GenDB web frontend. It can be used for a distributed manual genome annotation.
• GenDB GUI includes the sources of the graphical user interface written in Gtk. This frontend provides some enhanced functionality and it has more features than the web interface.

The following sections contain detailed information about each package and how to use it for annotating a genome. You can also find some documentation for software developers and system administrators in separate Wiki sections. If you are using the GenDB system for the first time, you should also read the Terms and Concepts section where the conceptual details of the system are explained.

Installation

• Installation Guide
• Installation FAQ

Documentation

• /CoreDocumentation
• /WebDocumentation
• /GUIDocumentation
• /DeveloperDocumentation
• /AdministratorDocumentation

General

• /FeatureTable
• /TermsAndConcepts
• /FuturePlans

Other Issues

For more information about project setup, license, application examples, and publications, please go to the GenDB website.

Contact

Please send an e-mail for account requests or questions concerning the use of GenDB to: MailTo(gendb AT cebitec DOT uni DASH bielefeld DOT de)

For bug reports, please use our bug reporting system BugZilla.

Authors: Jomuna V. Choudhuri, Alexander Goesmann