Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC).
BACKGROUND
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, CO(2) 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.
Rahman
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SA
Cologne University BioInformatics Center (CUBIC) and Institute of Biochemistry, Zülpicher Strasse 47, 50674 Köln, Germany.
Advani
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Schunk
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Schrader
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Schomburg
Dietmar
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D000465:Algorithms; D003198:Computer Simulation; D016208:Databases, Factual; D004734:Energy Metabolism / Q000502:physiology; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D020407:Internet; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
D029968:Escherichia coli Proteins; D014157:Transcription Factors