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 clusters of varying degrees 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 keywords such as those provided by SWISS-PROT and InterPro. ProtoNet can be used for function prediction, for defining superfamilies and subfamilies and for large-scale protein annotation purposes.
Original language | English |
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Pages (from-to) | 348-352 |
Number of pages | 5 |
Journal | Nucleic Acids Research |
Volume | 31 |
Issue number | 1 |
DOIs | |
State | Published - 1 Jan 2003 |
Bibliographical note
Funding Information:This work was supported by the Israeli Ministry of Defense, the Israeli Ministry of Science and by the Horowitz Foundation.