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

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 prote...

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Bibliographic Details
Published in:Bioinformatics 2005-11, Vol.21 (21), p.3963-3969
Main Authors: Guda, Chittibabu, Subramaniam, Shankar
Format: Article
Language:English
Subjects:
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
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Summary: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.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bti650