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Bioinformatics Advance Access originally published online on November 30, 2004
Bioinformatics 2005 21(7):1189-1193; doi:10.1093/bioinformatics/bti116
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)

S. A. Rahman , P. Advani , R. Schunk , R. Schrader and Dietmar Schomburg *

Cologne University BioInformatics Center (CUBIC) and Institute of Biochemistry Zülpicher Strasse 47, 50674 Köln, Germany

*To whom correspondence should be addressed.

Motivation: Pathway Hunter Tool (PHT), 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 Graphs, Network and Algorithm. Springer-Verlag, Berlin), average alternate path and the top 10 hubs in the metabolic network. The comparative study of metabolic connectivity and observing the cross talk between metabolic pathways among 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: PHT is accessible at http://www.pht.uni-koeln.de

Contact: d.schomburg{at}uni-koeln.de


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