CARMEN

CARMEN reconstructs metabolic networks in silico from microbial genomic sequence data generated by new sequencing technologies to enable functional interpretation and comparative genome analysis.

Key Features:

• In Silico Reconstruction: CARMEN automates reconstruction of metabolic networks from genomic data and generates network models.
• Visualization Capabilities: The software supports visualization of derived metabolic networks using pathway information from the KEGG database or user-defined SBML templates.
• Comparative Genomics Support: CARMEN performs comparative genomic analyses to compare and visualize metabolic pathways across different organisms.

Scientific Applications:

• Functional Context Interpretation: Reconstruction of pathways such as glycolysis and related reactions to interpret metabolic capabilities of organisms like Xanthomonas campestris pv. campestris B100.
• Comparative Analysis: Comparison of carbohydrate metabolism among corynebacteria to support comparative genomics studies.

Methodology:

Automated reconstruction converts sequence data into metabolic network models stored in the SBML (Systems Biology Markup Language) format; visualization uses KEGG pathway information or user-defined SBML templates; comparative genomic analyses operate on the reconstructed networks.