Nucleic Acids Research Advance Access originally published online on May 5, 2007
Nucleic Acids Research 2007 35(Web Server issue):W613-W618; doi:10.1093/nar/gkm287
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W613-W618
© 2007 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.
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MetaPath Online: a web server implementation of the network expansion algorithm
1Department of Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany and 2University Hospital Charité Berlin, Institute of Biochemistry, Monbijoustrasse 2, 10117 Berlin, Germany
*To whom correspondence should be addressed. Email: oliver.ebenhoeh{at}rz.hu-berlin.de
Received January 30, 2007. Revised March 28, 2007. Accepted April 12, 2007.
We designed a web server for the analysis of biosynthetic capacities of metabolic networks. The implementation is based on the network expansion algorithm and the concept of scopes. For a given network and predefined external resources, called the seed metabolites, the scope is defined as the set of products which the network is in principle able to produce. Through the web interface the user can select a variety of metabolic networks or provide his or her own list of reactions. The information on the organism-specific networks has been extracted from the KEGG database. By choosing an arbitrary set of seed compounds, the user can obtain the corresponding scopes. With our web server application we provide an easy to use interface to perform a variety of structural and functional network analyses. Problems that can be addressed using the web server include the calculation of synthesizing capacities, the visualization of synthesis pathways, functional analysis of mutant networks or comparative analysis of related species. The web server is accessible through http://scopes.biologie.hu-berlin.de.
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