NETAL

NETAL: a new graph-based method for global alignment of protein–protein interaction networks. 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. Availability: Binaries supported on linux are freely available for download at http://www.bioinf.cs.ipm.ir/software/netal.