Global Alignment of Protein-Protein Interaction Networks: A Survey

IEEE/ACM Trans Comput Biol Bioinform. Jul-Aug 2016;13(4):689-705. doi: 10.1109/TCBB.2015.2474391. Epub 2015 Aug 28.


In this paper, we survey algorithms that perform global alignment of networks or graphs. Global network alignment aligns two or more given networks to find the best mapping from nodes in one network to nodes in other networks. Since graphs are a common method of data representation, graph alignment has become important with many significant applications. Protein-protein interactions can be modeled as networks and aligning these networks of protein interactions has many applications in biological research. In this survey, we review algorithms for global pairwise alignment highlighting various proposed approaches, and classify them based on their methodology. Evaluation metrics that are used to measure the quality of the resulting alignments are also surveyed. We discuss and present a comparison between selected aligners on the same datasets and evaluate using the same evaluation metrics. Finally, a quick overview of the most popular databases of protein interaction networks is presented focusing on datasets that have been used recently.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Computational Biology / methods*
  • Humans
  • Protein Interaction Mapping / methods*
  • Protein Interaction Maps