A System For Motif Search In Biological Networks

Abstract

In this work, we investigate an important problem from the biology field, which consists in searching for specific patterns, named motifs, in networks which represent certain biological interactions, such as metabolic networks, regulatory networks or Protein-Protein Interaction (PPI) networks. Two linear integer models are proposed, one of them using the concept of representatives. We present computational experiments made with instances generated from PPI networks with approximately 8.000 proteins and 29.000 interactions among them. As experimentally verified, the two proposed models were able to solve all instances in a very satisfactory amount of computational time.