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Bioinformatics Advance Access originally published online on May 4, 2009
Bioinformatics 2009 25(15):1989-1990; doi:10.1093/bioinformatics/btp287
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MetNetAligner: a web service tool for metabolic network alignments

Qiong Cheng , Robert Harrison and Alexander Zelikovsky *

Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA

* To whom correspondence should be addressed.


  Abstract

Summary: The accumulation of high-throughput genomic, proteomic and metabolical data allows for increasingly accurate modeling and reconstruction of metabolic networks. Alignment of the reconstructed networks can help to catch model inconsistencies and infer missing elements. In this note, we present the web service tool MetNetAligner which aligns metabolic networks, taking in account the similarity of network topology and the enzymes' functions. It can be used for predicting unknown pathways, comparing and finding conserved patterns and resolving ambiguous identification of enzymes. The tool supports several alignment options including allowing or forbidding enzyme deletion and insertion. It is based on a novel scoring scheme which measures enzyme-to-enzyme functional similarity and a fast algorithm which efficiently finds optimal mappings from a directed graph with restricted cyclic structure to an arbitrary directed graph.

Availability: MetNetAligner is available as web-server at: http://alla.cs.gsu.edu:8080/MinePW/pages/gmapping/GMMain.html.

Contact: alexz{at}cs.gsu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Limsoon Wong

Received on December 30, 2008; revised on April 24, 2009; accepted on April 24, 2009

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