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