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 protein

SUBMITTER: Rappoport N 

PROVIDER: S-EPMC3245180 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature