/isorank

IsoRank family of PPI Network Alignment Algorithms

Primary LanguageC++GNU General Public License v3.0GPL-3.0

IsoRank & IsoRank-N

The IsoRank family of Network Alignment Algorithms

The IsoRank and IsoRank-N algorithms are designed for global alignment of multiple graphs against each other, especially when an independent measure of node similarity across the various graphs is available. They were designed for global alignment of protein-protein interaction (PPI) networks across species, with the sequence similarity of proteins being the node similarity measure. However, these are general algorithms that have been used for network alignment in other domains too (e.g., alignment of electron microscopy images).

The executable is available at: http://isorank.csail.mit.edu

  • The original IsoRank algorithm was presented in Singh, Xu and Berger (RECOMB 2007 & PNAS 2008) and is made available here as IsoRank-Orig-2008

  • An improved and more generalized version, as the IsoRank-N algorithm, were presented by Liao et al. (Bioinformatics 2009). The original implementation was by Prof. Chung-Shou Liao and Kanghao Lu. Later, students in Prof. Liao's lab made further speed improvements to the algorithm, especially Cheng-Yu Ma and Guan-Chung Chen. This codebase is made available here as IsoRankN-2018.

  • The executable available at http://isorank.csail.mit.edu corresponds to the IsoRank-N algorithm.

  • A database of functional orthologs, as predicted by IsoRank, is available at http://isobase.csail.mit.edu

References:

  • R Singh, J Xu, B Berger. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proceedings of the National Academy of Sciences 105 (35), 12763-12768

  • CS Liao, K Lu, M Baym, R Singh, B Berger. IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25 (12), i253-i258

  • D Park, R Singh, M Baym, CS Liao, B Berger. IsoBase: a database of functionally related proteins across PPI networks. Nucleic acids research 39 (suppl_1), D295-D300

  • R Singh, J Xu, B Berger. Pairwise global alignment of protein interaction networks by matching neighborhood topology. Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2007

  • R Singh, J Xu, B Berger. Global alignment of multiple protein interaction networks. Pac Symp of Biocomputing 2008, 303-314