Eva Trost, Jessica Schneider, Jochen Blom, Andreas Tauch, Alexander Goesmann

Center for Biotechnology, Bielefeld University, Germany

etrost@cebitec.uni-bielefeld.de

Newly developed ultrafast sequencing strategies provide efficient access to huge amounts of microbial genome sequences. The open source prokaryotic genome annotation system GenDB can be used for administration, processing and visualization of the generated data. One challenge after assembly and annotation is the establishment of an automated and fast functional analysis pipeline based on comparative genome analysis approaches. Therefore, the tools CARMEN and EDGAR have been developed. CARMEN (Comparative Analysis and Reconstruction of Metabolic Networks) supports the fast de novo reconstruction of metabolic pathways. De novo pathway reconstruction is based on KGML-files of KEGG pathway maps in combination with genome annotation data. Furthermore, curated models can be mapped onto a reference genome template. Thus, the results of reciprocal best BLAST hits between all genes of a newly sequenced species and the reference genome are employed. The output of CARMEN is a file compliant to the standardized SBML-format. As an XML-based exchange format it can be visualized by the CellDesigner software to get a quick overview of metabolic networks. This organism-specific network model of individual or large scale metabolic pathways can be reconstructed based on genome annotation data which can be obtained from NCBI GenBank files or alternatively from a local installation of GenDB. CARMEN provides a user-friendly way to manipulate (add, remove, change) the reconstructed pathways. EDGAR (Efficient Database framework for comparative Genome Analysis using BLAST score Ratios) was developed to accomplish the major tasks in comparative genomics like the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. The integration of CARMEN and EDGAR facilitates a special comparative metabolic network visualization and allows to rapidly detect the special genomic features of a species of interest.