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New Brochure: Facetten der Genomforschung
Wissenschaftler entschlüsseln die Baupläne des Lebens (german; pdf; 12,3 Mb)
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Research project: TPMG Bielefeld
Technology Platform Bioinformatics
Project time: 01.04.10-31.12.13
Cluster coordinator: Dr. Alexander Goesmann, Universität Bielefeld, Bielefeld
Project partners: (alphabetical order)
   Dr. Alexander Goesmann, Universität Bielefeld
   Prof. Dr. Alfred Pühler, Universität Bielefeld

      Overview subprojects

Research in the field of genome and metagenome analysis is currently pushed forward by ultrafast high-throughput sequencing technologies of the companies 454 Life Sciences, Illumina Inc. and Applied Biosciences. The main benefit of these new technologies is a dramatical reduction in both the sequencing costs and the complexity of the required experimental setups. In a multitude of sequencing projects the rewards of these new technologies could already be reaped – a development, however, that has also resulted in a vast increase in sequence data just waiting to be analyzed. The requirements placed on bioinformatics include not only the assembly and functional annotation of pro- and eukaryotic sequence data but also the comparative analysis of closely related species or strains as well as studies of the composition of microbial communities taken from different ecosystems.
The Technology Platform Bioinformatics can look back on many years of expertise in the computational processing of genomic and post-genomic datasets. Already during the research initiatives "GenoMik" and "GenoMik-Plus" funded by the German Federal Ministry of Education and Research, the platform served as a central bioinformatics service provider for project partners. Within the GenoMik-Transfer initiative, collaboration partners are offered a comprehensive infrastructure for data storage and analysis. A high performance compute infrastructure facilitates the detailed processing of experimental data in a timely manner. For this purpose, the Technology Platform Bioinformatics provides access to a variety of bioinformatics tools and software applications ranging from functional genome analysis and metagenomics to transcriptomics, metabolomics, and proteomics. In our application development special attention is always paid to the design of user-friendly interfaces and an easy and straight-forward usability. Currently, the list of software packages provided by Bielefeld includes i) GenDB for the annotation and maintenance of complete genomes (Meyer et al., 2003), ii) SAMS for the analysis and management of individual sequences (Bekel et al., 2009), iii) EDGAR for the comparative analysis of closely related genomes (Blom et al., 2009), iv) EMMA as a platform for the processing of transcriptome datasets (Dondrup et al., 2009) as well as a wide range of further applications from the fields metagenomics, proteomics and metabolomics (
If you have any questions, don't hesitate to contact:
Dr. Alexander Goesmann, eMail: agoesman (at)


F. Meyer, A. Goesmann, A.C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, A. Pühler (2003) GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31(8): 2187-95.
T. Bekel, K. Henckel, H. Küster, F. Meyer, V. Mittard Runte, H. Neuweger, D. Paarmann, O. Rupp, M. Zakrzewski, A. Pühler, J. Stoye, A. Goesmann (2009) The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. J Biotechnol 140(1-2): 3-12.
J. Blom, S. P. Albaum, D. Doppmeier, A. Pühler, F. J. Vorhölter, M. Zakrzewski, A. Goesmann (2009) EDGAR: A software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10(1): 154.
M. Dondrup, S. P. Albaum, T. Griebel, K. Henckel, S. Jünemann, T. Kahlke, C. K. Kleindt, H. Küster, B. Linke, D. Mertens, V. Mittard Runte, H. Neuweger, K. J. Runte, A. Tauch, F. Tille, A. Pühler, A. Goesmann (2009) EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10(1): 50.