Nucleic Acids Research, 2005, Vol. 33, Database issue D216-D218
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
ProtoNet 4.0: A hierarchical classification of one million protein sequences
Department of Biological Chemistry, Institute of Life Sciences and 1 School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
* To whom correspondence should be addressed at The Hebrew University, Department of Biological Chemistry, Givat Ram Campus, Jerusalem, Israel, 91904. Tel: +972 2 6585433; Fax: +972 2 6586448; Email: kaplann{at}cc.huji.ac.il
Received September 10, 2004; Accepted September 14, 2004
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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