title: ProtoNet 4.0: a hierarchical classification of one million protein sequences.
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.
authors.affiliation: Department 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
authors.forename: Noam
authors.initials: N
authors.lastname: Kaplan
authors.forename: Ori
authors.initials: O
authors.lastname: Sasson
authors.forename: Uri
authors.initials: U
authors.lastname: Inbar
authors.forename: Moriah
authors.initials: M
authors.lastname: Friedlich
authors.forename: Menachem
authors.initials: M
authors.lastname: Fromer
authors.forename: Hillel
authors.initials: H
authors.lastname: Fleischer
authors.forename: Elon
authors.initials: E
authors.lastname: Portugaly
authors.forename: Nathan
authors.initials: N
authors.lastname: Linial
authors.forename: Michal
authors.initials: M
authors.lastname: Linial
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D051379:Mice; D011506:Proteins / Q000737:chemistry / Q000145:classification*; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins