title: NETAL: a new graph-based method for global alignment of protein-protein interaction networks.
abstract: BACKGROUND
  The interactions among proteins and the resulting networks of such interactions have a central role in cell biology. Aligning these networks gives us important information, such as conserved complexes and evolutionary relationships. Although there have been several publications on the global alignment of protein networks; however, none of proposed methods are able to produce a highly conserved and meaningful alignment. Moreover, time complexity of current algorithms makes them impossible to use for multiple alignment of several large networks together.
  
  
  RESULTS
  We present a novel algorithm for the global alignment of protein-protein interaction networks. It uses a greedy method, based on the alignment scoring matrix, which is derived from both biological and topological information of input networks to find the best global network alignment. NETAL outperforms other global alignment methods in terms of several measurements, such as Edge Correctness, Largest Common Connected Subgraphs and the number of common Gene Ontology terms between aligned proteins. As the running time of NETAL is much less than other available methods, NETAL can be easily expanded to multiple alignment algorithm. Furthermore, NETAL overpowers all other existing algorithms in term of performance so that the short running time of NETAL allowed us to implement it as the first server for global alignment of protein-protein interaction networks.
  
  
  BACKGROUND
  Binaries supported on linux are freely available for download at http://www.bioinf.cs.ipm.ir/software/netal.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
authors.forename: Behnam
authors.initials: B
authors.lastname: Neyshabur
authors.forename: Ahmadreza
authors.initials: A
authors.lastname: Khadem
authors.forename: Somaye
authors.initials: S
authors.lastname: Hashemifar
authors.forename: Seyed Shahriar
authors.initials: SS
authors.lastname: Arab
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D006801:Humans; D025941:Protein Interaction Mapping / Q000379:methods*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D016415:Sequence Alignment; D012984:Software
chemical_list: D029701:Saccharomyces cerevisiae Proteins