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Bioinformatics Advance Access originally published online on February 8, 2005
Bioinformatics 2005 21(10):2558-2559; 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{at}oupjournals.org

Protein function prediction using the Protein Link EXplorer (PLEX)

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

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

*To whom correspondence should be addressed.

Summary: We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the 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

Contact: marcotte{at}icmb.utexas.edu


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