Paper Info
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.
Year
DOI
Venue
2012
10.1093/nar/gkr1027
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
nucleic,algorithms,cluster analysis,metagenome,internet,proteins
Data structure,Annotation,Biology,UniProt,Theoretical computer science,Family tree,Tree structure,Bioinformatics,Molecular Sequence Annotation,Cluster analysis,Genetics,InterPro
Journal
Volume
Issue
ISSN
40
D1
0305-1048
Citations 
PageRank 
References 
5
0.46
26
Authors
5
Name
Order
Citations
PageRank
Nadav Rappoport1213.08
Solange Karsenty2305.84
Amos Stern360.82
Nati Linial43872602.77
Michal Linial51502149.92