CARMEN- Comparative Analysis and Reconstruction of MEtabolic Networks
KGML-based model generation
CARMEN provides the generation of KGML-based models derived from KEGG database information. They are combined with annotation data such as EC numbers, gene identifiers and gene names of a chosen organism. If there exists more than one annotated gene with identical EC number, CARMEN creates a new symbol for each of these genes close to each other. The generated metabolic networks are stored in the standardized SBML format to enable the subsequent editing and extension of chosen networks. This allows manual verification of pathways, which may get reconstructed in a semi-finished state in case of incomplete genome annotation data or database inconsistencies.
One application example is the reconstruction of the glycolysis pathway of Xanthomonas campestris pv. campestris B100 (Figure 1).
Beyond the basic KGML-based reconstruction, various options can be used to affect the output of the locally installable version of CARMEN:
- Integration of cofactors
- Choice of metabolite abbreviations
- Merging multiple enzyme symbols
Figure 1: Automatically KGML-based reconstructed pathway based on the KGML file of the glycolysis (KEGG map00010) using CARMEN visualized by CellDesigner. Lacking genes are represented by grey symbols displaying the EC number of the encoded protein.
Download SBML file of X. campestris