Title

Protonet 4.0: A Hierarchical Classification of One Million Protein Sequences

Publication Type

Journal Article

Publication Date

2005

Abstract

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.

Discipline

Bioinformatics | Computer Sciences

Research Areas

Intelligent Systems and Decision Analytics

Publication

Nucleic Acids Research

Volume

33

Issue

Suppl. 1

First Page

D216

Last Page

D218

ISSN

0305-1048

Identifier

10.1093/nar/gki007

Publisher

Oxford

Additional URL

http://dx.doi.org/10.1093/nar/gki007