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Bioinformatics Advance Access published online on July 16, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn360
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Torsten Blum a,* and Oliver Kohlbacher a

aDiv. for Simulation of Biological Systems, ZBIT/WSI, University of Tübingen, Germany

*To whom correspondence should be addressed. Torsten Blum, blum{at}informatik.uni-tuebingen.de


  Abstract

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{at}informatik.uni-tuebingen.de

Supplementary material: Supplementary details are available at http://www-bs.informatik.uni-tuebingen.de/Services/MetaRoute

Associate Editor: Prof. Thomas Lengauer

Received on February 20, 2008; revised on July 8, 2008; accepted on July 14, 2008

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