MetaPath Online: A web server implementation of the network expansion algorithm

Thomas Handorf, Oliver Ebenhoeh

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)W613-W618
Number of pages6
JournalNucleic Acids Research
Volume35
Issue numbersupp. 2
DOIs
Publication statusPublished - 1 Jul 2007

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Keywords

  • adenosine triphosphate
  • algorithms
  • computational biology
  • computer graphics
  • gene expression profiling
  • information storage and retrieval
  • internet
  • metabolism
  • models, biological
  • software
  • user-computer Interface

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