NetCoffee2: A Novel Global Alignment Algorithm for Multiple PPI Networks Based on Graph Feature Vectors

  • Jialu Hu
  • Junhao He
  • Yiqun Gao
  • Yan Zheng
  • Xuequn ShangEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10955)


Network alignment provides a fast and effective framework to automatically identify functionally conserved proteins in a systematic way. However, due to the fast growing biological data, there is an increasing demand for more accurate and efficient tools to deal with multiple PPI networks. Here, we present a novel global alignment algorithm NetCoffee2 to discover functionally conserved proteins. To test the algorithm performance, NetCoffee2 and several existing algorithms were applied on eight real biological datasets. Results show that NetCoffee2 is superior to IsoRankN, NetCoffee and multiMAGNA++ in terms of both coverage and consistency. The binary and source code are freely available at


PPI network alignment Simulated annealing Functionally conserved proteins 



This project has been funded by the National Natural Science Foundation of China (Grant No. 61332014 and 61702420); the China Postdoctoral Science Foundation (Grant No. 2017M613203); the Natural Science Foundation of Shaanxi Province (Grant No. 2017JQ6037); the Fundamental Research Funds for the Central Universities (Grant No. 3102018zy032).


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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Jialu Hu
    • 1
  • Junhao He
    • 1
  • Yiqun Gao
    • 1
  • Yan Zheng
    • 1
  • Xuequn Shang
    • 1
    Email author
  1. 1.School of Computer ScienceNorthwestern Polytechnical UniversityXi’anChina

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