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In molecular biology, the comparative analysis of organisms exhibiting different phenotypes is still mostly performed on the level of genes. However, many genes encode proteins that are involved in complex metabolic pathways, whose functions result from the interplay of all involved enzymes. So to understand the phenotype of any living system, it is essential to not only investigate single genes in isolation, but also the metabolic pathway variant of the particular organisms under study.
(Oehm et al., 2008) Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res.