Clustering Protein Sequences through Modularity Optimization

Abstract:

Remote homology detection between protein sequences is one of the principal research objectives in structural and functional genomics.Proteins with similar structure and function but low sequence similarity consist of protein superfamily.Therefore,the detection of remote homologues is the task of identifying protein superfamily.In this manuscript,a clustering algorithm,called ModuleFind,based on network modularity was presented.The method maximizes the modularity of protein network to find the partitioning with strong community structure.The resulting algorithm gives high quality of clusters quantified by F-measure that combines precise and recall,in the experiments of the detection of the remote homologues based on the superfamily level of SCOP database.