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Updated: Aug 20, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
ProtoNet 4.0: a hierarchical classification of one million protein sequences
Noam Kaplan1, Ori Sasson, Uri Inbar
1Department of Biological Chemistry, Institute of Life Sciences and School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel. kaplann@cc.huji.ac.il
Abstract:
ProtoNet is an automatic hierarchical classification of the protein sequence space. In 2004, the ProtoNet (version 4.0) presents the analysis of over one million proteins merged from SwissProt and TrEMBL databases. In addition to rich visualization and analysis tools to navigate the clustering hierarchy, we incorporated several improvements that allow a simplified view of the scaffold of the proteins. An unsupervised, biologically valid method that was developed resulted in a condensation of the ProtoNet hierarchy to only 12% of the clusters. A large portion of these clusters was automatically assigned high confidence biological names according to their correspondence with functional annotations. ProtoNet is available at: http://www.protonet.cs.huji.ac.il.
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