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In Silico Biology 5, 0013 (2004); ©2005, Bioinformation Systems e.V.  

An algorithm for linear metabolic pathway alignment

Ming Chen* and Ralf Hofestädt

Bioinformatics / Medical Informatics, Technische Fakultät, Universität Bielefeld, Postfach 10 01 31, D-33501 Bielefeld, Germany

* Corresponding author; Email:

Edited by E. Wingender; received September 30, 2004; revised and accepted December 09, 2004; published February 05, 2005


Metabolic pathway alignment represents one of the most powerful tools for comparative analysis of metabolism. It involves recognition of metabolites common to a set of functionally-related metabolic pathways, interpretation of biological evolution processes and determination of alternative metabolic pathways. Moreover, it is of assistance in function prediction and metabolism modeling. Although research on genomic sequence alignment is extensive, the problem of aligning metabolic pathways has received less attention. We are motivated to develop an algorithm of metabolic pathway alignment to reveal the similarities between metabolic pathways. A new definition of the metabolic pathway is introduced. The algorithm has been implemented into the PathAligner system; its web-based interface is available at

Keywords: metabolic pathways, alignment, algorithm, PathAligner