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Analysis of metabolic pathways is a central topic in understanding the relationship between genotype and phenotype. The rapid accumulation of biological data provides the possibility of studying metabolic pathways both at the genomic and metabolic levels. Our motivation is to develop a conceptual framework and computational system that will allow retrieval of metabolic information and prediction of metabolic pathways. In this paper, we introduce a metabolic pathway prediction framework that extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. It provides an easy-to-use interface to retrieve, display, and manipulate metabolic information. The system has been implemented into PathAligner, available at http://bibiserv.techfak.uni-bielefeld.de/pathaligner/.