title: ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree.
abstract: ProtoNet 6.0 (http://www.protonet.cs.huji.ac.il) is a data structure of protein families that cover the protein sequence space. These families are generated through an unsupervised bottom-up clustering algorithm. This algorithm organizes large sets of proteins in a hierarchical tree that yields high-quality protein families. The 2012 ProtoNet (Version 6.0) tree includes over 9 million proteins of which 5.5% come from UniProtKB/SwissProt and the rest from UniProtKB/TrEMBL. The hierarchical tree structure is based on an all-against-all comparison of 2.5 million representatives of UniRef50. Rigorous annotation-based quality tests prune the tree to most informative 162,088 clusters. Every high-quality cluster is assigned a ProtoName that reflects the most significant annotations of its proteins. These annotations are dominated by GO terms, UniProt/Swiss-Prot keywords and InterPro. ProtoNet 6.0 operates in a default mode. When used in the advanced mode, this data structure offers the user a view of the family tree at any desired level of resolution. Systematic comparisons with previous versions of ProtoNet are carried out. They show how our view of protein families evolves, as larger parts of the sequence space become known. ProtoNet 6.0 provides numerous tools to navigate the hierarchy of clusters.
authors: School of Computer Science and Engineering, Institute of Life Sciences, The Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, 91904 Israel.
authors: Nadav
authors: N
authors: Rappoport
authors: Solange
authors: S
authors: Karsenty
authors: Amos
authors: A
authors: Stern
authors: Nathan
authors: N
authors: Linial
authors: Michal
authors: M
authors: Linial
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D030562:Databases, Protein; D020407:Internet; D054892:Metagenome; D058977:Molecular Sequence Annotation; D011506:Proteins / Q000145:classification*; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins