title: Global network alignment using multiscale spectral signatures.
abstract: BACKGROUND
  Protein interaction networks provide an important system-level view of biological processes. One of the fundamental problems in biological network analysis is the global alignment of a pair of networks, which puts the proteins of one network into correspondence with the proteins of another network in a manner that conserves their interactions while respecting other evidence of their homology. By providing a mapping between the networks of different species, alignments can be used to inform hypotheses about the functions of unannotated proteins, the existence of unobserved interactions, the evolutionary divergence between the two species and the evolution of complexes and pathways.
  
  
  RESULTS
  We introduce GHOST, a global pairwise network aligner that uses a novel spectral signature to measure topological similarity between subnetworks. It combines a seed-and-extend global alignment phase with a local search procedure and exceeds state-of-the-art performance on several network alignment tasks. We show that the spectral signature used by GHOST is highly discriminative, whereas the alignments it produces are also robust to experimental noise. When compared with other recent approaches, we find that GHOST is able to recover larger and more biologically significant, shared subnetworks between species.
  
  
  BACKGROUND
  An efficient and parallelized implementation of GHOST, released under the Apache 2.0 license, is available at http://cbcb.umd.edu/kingsford_group/ghost
  
  
  BACKGROUND
  rob@cs.umd.edu.
authors.affiliation: Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies and Department of Computer Science, University of Maryland, College Park, MD 20742, USA. rob@cs.umd.edu
authors.forename: Rob
authors.initials: R
authors.lastname: Patro
authors.forename: Carl
authors.initials: C
authors.lastname: Kingsford
mesh_terms: D000465:Algorithms; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D011506:Proteins / Q000032:analysis
chemical_list: D011506:Proteins