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Bioinformatics Advance Access published online on June 9, 2006
Bioinformatics, 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
Received April 12, 2006
Accepted May 16, 2006

Applications note

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

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

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; Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, China

* To whom correspondence should be addressed.
Maikun Teng, E-mail: mkteng{at}ustc.edu.cn


  Abstract

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 E. coli PIN against the H. pylori PIN and (2) the S. cerevisiae PIN against the C. 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.

Associate Editor: Jonathan Wren

{dagger} These authors contribute equally to the work.


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