NetCoffee

NetCoffee is a software tool that allows for the global alignment of multiple protein-protein interaction networks, and was developed to identify functionally conserved proteins across species. It uses a weighted bipartite graph approach, similar to T-Coffee, and maximizes a target function using simulated annealing. NetCoffee was tested on four real datasets and outperformed existing alignment tools in terms of speed and identifying biologically meaningful alignments.

Topic

Proteins;Protein interactions;Molecular interactions, pathways and networks

Detail

  • Operation: Global alignment

  • Software interface: Command-line user interface

  • Language: C++

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: China Scholarship Council (CSC).

  • Input: NETCOFFEE

  • Output: -

  • Contact: jialu.hu@fu-berlin.de

  • Collection: -

  • Maturity: Stable

Publications

  • NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.
  • Hu J, et al. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. 2014; 30:540-8. doi: 10.1093/bioinformatics/btt715
  • https://doi.org/10.1093/bioinformatics/btt715
  • PMID: 24336806
  • PMC: -

Download and documentation

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