MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization

Summary: We present MetaRoute, an efficient search algorithm based on atom mapping rules and path weighting schemes that returns relevant or textbook-like routes between a source and a product metabolite within seconds for genome-scale networks. Its speed allows the algorithm to be used interactively through a web interface to visualize relevant routes and local networks for one or multiple organisms based on data from KEGG. Availability: http://www-bs.informatik.uni-tuebingen.de/Services/MetaRoute. Contact: blum@informatik.uni-tuebingen.de Supplementary information: Supplementary details are available at http://www-bs.informatik.uni-tuebingen.de/Services/MetaRoute

[1]  Oliver Kohlbacher,et al.  Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks , 2008, J. Comput. Biol..

[2]  Shoshana J. Wodak,et al.  Metabolic PathFinding: inferring relevant pathways in biochemical networks , 2005, Nucleic Acids Res..

[3]  Falk Schreiber,et al.  Dynamic exploration and editing of KEGG pathway diagrams , 2007, Bioinform..

[4]  Christina Backes,et al.  BN++ - A Biological Information System , 2006, J. Integr. Bioinform..

[5]  Oliver Ebenhöh,et al.  MetaPath Online: a web server implementation of the network expansion algorithm , 2007, Nucleic Acids Res..

[6]  Masanori Arita,et al.  Metabolic reconstruction using shortest paths , 2000, Simul. Pract. Theory.

[7]  Rainer Schrader,et al.  Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC) , 2005, Bioinform..

[8]  Erich Bornberg-Bauer,et al.  BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks , 2002, ECCB.

[9]  Francisco J. Planes,et al.  A critical examination of stoichiometric and path-finding approaches to metabolic pathways , 2008, Briefings Bioinform..

[10]  Stefan Schuster,et al.  Systems biology Metatool 5.0: fast and flexible elementary modes analysis , 2006 .

[11]  Minoru Kanehisa,et al.  Toward Pathway Engineering: A New Database of Genetic and Molecular Pathways , 1997 .

[12]  Masanori Arita.  In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. , 2003, Genome research.

[13]  D. Fell,et al.  Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.

[14]  Christina Backes,et al.  BNDB – The Biochemical Network Database , 2007, BMC Bioinformatics.

[15]  David Eppstein,et al.  Finding the k Shortest Paths , 1999, SIAM J. Comput..