Gradually expanding neighborhoods with adjustment (GENA) is a new algorithm for the computational prediction of protein complexes which makes the realistic assumption that proteins participate in multiple protein complexes and cellular functions. GENA gradually expands neighborhoods in a graph starting from highly informative “seed“nodes. GENA considers proteins as multifunctional molecules allowing them to participate in more than one protein complex. In addition, GENA accepts weighted PPI graphs by using a weighted evaluation function for each cluster.
The implementation for Matlab environment is available at Github: https://github.com/InSyBio/gena/.