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Vol. 12, Issue 5, 785-794, May 2002

LETTER
Large-Scale Protein Annotation through Gene Ontology

Hanqing Xie,1,3 Alon Wasserman,1 Zurit Levine,2 Amit Novik,2 Vladimir Grebinskiy,1 Avi Shoshan,1 and Liat Mintz1,3

1 Compugen Inc., Jamesburg, New Jersey 08831, USA; 2 Compugen Ltd., Tel Aviv 69512, Israel

Recent progress in genomic sequencing, computational biology, and ontology development has presented an opportunity to investigate biological systems from a unique perspective, that is, examining genomes and transcriptomes through the multiple and hierarchical structure of Gene Ontology (GO). We report here our development of GO Engine, a computational platform for GO annotation, and analysis of the resultant GO annotations of human proteins. Protein annotation was centered on sequence homology with GO-annotated proteins and protein domain analysis. Text information analysis and a multiparameter cellular localization predictive tool were also used to increase the annotation accuracy, and to predict novel annotations. The majority of proteins corresponding to full-length mRNA in GenBank, and the majority of proteins in the NR database (nonredundant database of proteins) were annotated with one or more GO nodes in each of the three GO categories. The annotations of GenBank and SWISS-PROT proteins are available to the public at the GO Consortium web site.

3 Corresponding authors.

12:785-794 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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