MAVisto: A Tool for Biological Network Motif Analysis

Abstract

Data from high-throughput experimental methods are currently being used to construct complex biological networks. These include regulatory gene networks, regulatory protein–DNA networks, protein–protein interaction networks, or metabolic networks. Independent of its type, every network can be characterized by a number of parameters such as number of nodes, number of edges connecting nodes, direction and weight of edges, in- and out-degree of nodes, etc. One can draw an analogy of such rather simple network parameters to the primary sequence of proteins or nucleic acids. More insight can be gained by an analysis of the secondary and tertiary structure of biomolecules, which often contain motifs. The same holds for biological networks. The occurrence and frequency of certain motifs or pattern characterize the topology and often the functional space of a network. Here, we describe the utilization of the free software MAVisto, which was designed to mine networks for typical motifs by combining a flexible motif search algorithm with interactive exploration methods and sophisticated visualization techniques.