ProtoNet : Navigating the Hierarchical Clustering of the Protein Space

The ProtoNet site provides an automatic hierarchical clustering of the protein space. The clustering is based on an all-against-all BLAST similarity test. With this similarity measure we proceed to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a hierarchy of clusters of varying degrees of granularity. This clustering can be used for function prediction, for define superfamilies and subfamilies and for large-scale protein annotation purposes. ProtoNet is accessible in the form of an interactive Web site at http://www.protonet.cs.huji.ac.il.