cytokavosh a cytoscape plug-in for finding network motifs in large biological networkscytokavosh cytoscape插件查找网络主题大型生物网络.pdfVIP

CytoKavosh: A Cytoscape Plug-In for Finding Network Motifs in Large Biological Networks Ali Masoudi-Nejad*., Mitra Ansariola., Zahra Razaghi Moghadam Kashani, Ali Salehzadeh-Yazdi, Sahand Khakabimamaghani Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran Abstract Network motifs are small connected sub-graphs that have recently gathered much attention to discover structural behaviors of large and complex networks. Finding motifs with any size is one of the most important problems in complex and large networks. It needs fast and reliable algorithms and tools for achieving this purpose. CytoKavosh is one of the best choices for finding motifs with any given size in any complex network. It relies on a fast algorithm, Kavosh, which makes it faster than other existing tools. Kavosh algorithm applies some well known algorithmic features and includes tricky aspects, which make it an efficient algorithm in this field. CytoKavosh is a Cytoscape plug-in which supports us in finding motifs of given size in a network that is formerly loaded into the Cytoscape work-space (directed or undirected). High performance of CytoKavosh is achieved by dynamically linking highly optimized functions of Kavosh’s C++ to the Cytoscape Java program, which makes this plug-in suitable for analyzing large biological networks. Some significant attributes of CytoKavosh is efficiency in time usage and memory and having no limitation related to the implementation in motif size. CytoKavosh is implemented in a visual environment Cytoscape that is convenient for the users to interact and create visual options to analyze the structural behavior of a network. This plug-in can work on any given network and is very simple to use and generates graphical results of discovered motifs with a