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Bioinformatics Advance Access originally published online on June 9, 2006
Bioinformatics 2006 22(17):2175-2177; doi:10.1093/bioinformatics/btl287
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

NetAlign: a web-based tool for comparison of protein interaction networks

Zhi Liang 1,2,{dagger}, Meng Xu 1,2,{dagger}, Maikun Teng 1,2,* and Liwen Niu 1,2,*

1 Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science & Technology of China 96 Jinzhai Road, Hefei, Anhui 230027, China
2 Key Laboratory of Structural Biology, Chinese Academy of Sciences 96 Jinzhai Road, Hefei, Anhui 230027, China

*To whom correspondence should be addressed.

Summary: NetAlign is a web-based tool designed to enable comparative analysis of protein interaction networks (PINs). NetAlign compares a query PIN with a target PIN by combining interaction topology and sequence similarity to identify conserved network substructures (CoNSs), which may derive from a common ancestor and disclose conserved topological organization of interactions in evolution. To exemplify the application of NetAlign, we perform two genome-scale comparisons with (1) the Escherichia coli PIN against the Helicobacter pylori PIN and (2) the Saccharomyces cerevisiae PIN against the Caenorrhabditis elegans PIN. Many of the identified CoNSs correspond to known complexes; therefore, cross-species PIN comparison provides a way for discovery of conserved modules. In addition, based on the species-to-species differences in CoNSs, we reformulate the problems of protein–protein interaction (PPI) prediction and species divergence from a network perspective.

Availability: http://www1.ustc.edu.cn/lab/pcrystal/NetAlign

Supplementary Data: Supplementary data are available at Bioinformatics online.

Contact: mkteng{at}ustc.edu.cn, lwniu{at}ustc.edu.cn

Received on April 12, 2006; accepted on May 16, 2006

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