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Bioinformatics Advance Access published online on February 8, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti313
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received September 29, 2004
Revised February 6, 2005
Accepted February 7, 2005

Applications note

Protein function prediction using the Protein Link Explorer (PLEX)

Shailesh V. Date 1 and Edward M. Marcotte 2*

1 Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, 1 University Station, A4800 Austin, Texas 78712-1064, USA
2 Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, 1 University Station, A4800 Austin, Texas 78712-1064, USA; Department of Chemistry and Biochemistry University of Texas at Austin, 1 University Station, A4800 Austin, Texas 78712-1064, USA

* To whom correspondence should be addressed.
Edward M. Marcotte, E-mail: marcotte{at}icmb.utexas.edu


  Abstract

Summary: We introduce PLEX, a web-based environment that allows construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of ~350,000 predicted genes from 89 genomes, as a means of interactively identifying functionally-linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon, and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways.

Availability: http://bioinformatics.icmb.utexas.edu/plex.


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