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Metabolic pathway comparison software tools | Metabolic engineering data analysis

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.

Source text:
(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.

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TabPath / Tables for Metabolic Pathway
Simultaneously compares multiple pathways and genomes and constructs analytical reports. TabPath allows users to submit genomes and metabolic pathways. It is based on the utilization of the KEGG database. This tool is able to produce files simplifying comparison and evaluation of variations in metabolism in a predetermined organism selected by the researcher. It can return a map of all the proteins/genes of the respective organism present in the genome inputted.
An open-source software tool to support the manual comparison and curation of metabolic models. It combines gene annotations from GenBank files and other sources with information retrieved from the metabolic databases BRENDA and KEGG to produce a set of pathway diagrams and reports summarising the evidence for the presence of a reaction in a given organism’s metabolic network. By comparing multiple sources of evidence within a common framework, PathwayBooster assists the curator in the identification of likely false positive (misannotated enzyme) and false negative (pathway hole) reactions. Reaction evidence may be taken from alternative annotations of the same genome and/or a set of closely related organisms.
CPA / Comparative Pathway Analyzer
Allows users to realize metabolic pathway analysis. CPA aims at finding unique metabolic reaction content that is worth to be further analyzed. This tool provides a visualization engine for displaying differential metabolic reaction content resulting from comparing two sets of organisms. It provides an automated approach based on clustering techniques for finding an appropriate grouping. It uses a subdivision of the overall metabolic network into smaller subnetworks.
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