TARGET: a new method for predicting protein subcellular localization in eukaryotes

Authors:
Chittibabu Guda;Shankar Subramaniam
Affiliations:
Gen*NY*sis Center for Excellence in Cancer Genomics, State University of New York One Discovery Drive, Rensselaer, NY 12144-3456, USA;San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
Venue:
Bioinformatics
Year:
2005

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Abstract

Motivation: There is a scarcity of efficient computational methods for predicting protein subcellular localization in eukaryotes. Currently available methods are inadequate for genome-scale predictions with several limitations. Here, we present a new prediction method, pTARGET that can predict proteins targeted to nine different subcellular locations in the eukaryotic animal species. Results: The nine subcellular locations predicted by pTARGET include cytoplasm, endoplasmic reticulum, extracellular/secretory, golgi, lysosomes, mitochondria, nucleus, plasma membrane and peroxisomes. Predictions are based on the location-specific protein functional domains and the amino acid compositional differences across different subcellular locations. Overall, this method can predict 68--87% of the true positives at accuracy rates of 96--99%. Comparison of the prediction performance against PSORT showed that pTARGET prediction rates are higher by 11--60% in 6 of the 8 locations tested. Besides, the pTARGET method is robust enough for genome-scale prediction of protein subcellular localizations since, it does not rely on the presence of signal or target peptides. Availability: A public web server based on the pTARGET method is accessible at the URL http://bioinformatics.albany.edu/~ptarget. Datasets used for developing pTARGET can be downloaded from this web server. Source code will be available on request from the corresponding author. Contact: cguda@albany.edu Supplementary data: Accessible as online-only from the publisher.