ProtoNet: hierarchical classification of the protein space

Nucleic Acids Res. 2003 Jan 1;31(1):348-52. doi: 10.1093/nar/gkg096.

Abstract

The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a hierarchy of clusters of varying degrees of granularity. ProtoNet (version 1.3) is accessible in the form of an interactive web site at http://www.protonet.cs.huji.ac.il. ProtoNet provides navigation tools for monitoring the clustering process with a vertical and horizontal view. Each cluster at any level of the hierarchy is assigned with a statistical index, indicating the level of purity based on biological keywords such as those provided by SWISS-PROT and InterPro. ProtoNet can be used for function prediction, for defining superfamilies and subfamilies and for large-scale protein annotation purposes.

MeSH terms

  • Animals
  • Cluster Analysis
  • Databases, Protein*
  • Information Storage and Retrieval
  • Internet
  • Proteins / chemistry
  • Proteins / classification*
  • Proteins / physiology

Substances

  • Proteins