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International Journal of Genomics
Volume 2013 (2013), Article ID 670623, 11 pages
Research Article

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

1School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China
2Department of Computer and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
3Computer Science Department, North Carolina State University, Raleigh, NC 27696, USA

Received 22 December 2012; Revised 5 February 2013; Accepted 23 February 2013

Academic Editor: G. Pesole

Copyright © 2013 Wenhong Tian and Nagiza F. Samatova. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based on a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium, E. coli K12 and C. crescenttus, we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.