ProtoNet: hierarchical classification of the protein space

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Abstract
The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities E - score is used 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 cluster of varying degree of granularity. ProtoNet ( version 1.3) is accessible in the form of an interactive web site at http: / / www. protonet. cs. huji. ac. il. ProtoNet provides navigation tools for monitoring the clustering process with a vertical and horizontal view. Each cluster at any level of the hierarchy is assigned with a statistical index, indicating the level of purity based on biological keyword such as those provided by SWISS-PROT and InterPro. ProtoNet can be used for function prediction, for de ning superfamilies and subfamilies and for large-scale protein annotation purposes.