Tools for analysis of biochemical network topology

The biochemical networks can present the relationships between genes and gene products, proteins, metabolites and etc. The exploration of these networks helps to understand cellular processes, functions or properties of biological system. The growing size of interaction models of biological system building elements request determination of the most important topological measurements of given task and powerful automated software tools to perform the analysis. The network structure measures and properties are categorized in five groups: topological parameters, topological features, network metrics, network motifs and quantitative parameters of whole network structure. Topology analysis related features of software tools Cytoscape with plug-ins BiNoM and NetworkAnalyzer, VisANT, Biological Networks and CelNetAnalyser are reviewed to simplify the task-dependent choice. The applicability of software tools for calculation of 44 topological features is summarized. Research resulted in overview on biochemical network structure analysis, on used topological features with the following goals: 1) to accumulate the existing knowledge about the network structure analysis; 2) to provide a list of topological parameters and features; 3) to provide the information of the existing software tools for the structure analysis.