Bioinformatics Advance Access published online on November 30, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti116
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 Cologne University BioInformatics Center (CUBIC) & Institute of Biochemistry Zülpicher Strasse 47, 50674 Köln, Germany
* To whom correspondence should be addressed.
Motivation: Pathway Hunter Tool (PHT) (Syed Asad Rahman et al., 2004) is a fast, robust, and user friendly tool to analyse the shortest paths in metabolic pathways. The user can perform shortest path analysis for one or more organisms or can build virtual organisms (networks) using enzymes. Using PHT, the user can also calculate the average shortest path (Jungnickel, 2002), average alternate path and the top 10 hubs in the metabolic network. The comparative study of metabolic connectivity and the cross talk between metabolic pathways between various sequenced genomes is possible. Results: A new algorithm for finding the biochemically valid connectivity between metabolites in a metabolic network was developed and implemented. A predefined manual assignment of side metabolites (like ATP, ADP, Water, CO2 etc) and main metabolites is not necessary as the new concept uses chemical structure information (global and local similarity) between metabolites for identification of the shortest path. Availability: Pathway Hunter Tool (PHT) is accessible at http://www.pht.uni-koeln.de.
Revised October 21, 2004
Accepted October 21, 2004
Article
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
S. A. Rahman, E-mail: asad.rahman{at}uni-koeln.de
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