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PathAligner: metabolic pathway retrieval and alignment.

Ming Chen·Ralf Hofestädt
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Abstract

MOTIVATION: 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 at both the genomic and the metabolic levels. Retrieving metabolic pathways from current biological data sources, reconstructing metabolic pathways from rudimentary pathway components, and aligning metabolic pathways with each other are major tasks. Our motivation was to develop a conceptual framework and computational system that allows the retrieval of metabolic pathway information and the processing of alignments to reveal the similarities between metabolic pathways. RESULTS: PathAligner 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. PathAligner also provides an alignment method to compare the similarity between metabolic pathways. AVAILABILITY: PathAligner is available at http://bibiserv.techfak.uni-bielefeld.de/pathaligner.

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AlgorithmsDatabase Management SystemsDatabases, FactualGene Expression RegulationInformation Storage and RetrievalModels, BiologicalProteomeSequence AlignmentSignal TransductionSoftwareUser-Computer InterfaceEvaluation StudyJournal ArticleResearch Support, Non-U.S. Gov't

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Ming Chen, Ralf Hofestädt. 2004. PathAligner: metabolic pathway retrieval and alignment.. https://doi.org/10.2165/00822942-200403040-00006

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