Skip Navigation



Bioinformatics Advance Access published online on September 6, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti650
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/21/3963    most recent
bti650v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Guda, C.
Right arrow Articles by Subramaniam, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Guda, C.
Right arrow Articles by Subramaniam, S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received May 3, 2005
Revised August 26, 2005
Accepted August 26, 2005

Article

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

Chittibabu Guda 1* and Shankar Subramaniam 2

1 Gen*NY*sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY 12144-3456, USA; Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One University Place, Rensselaer, NY 12144, USA
2 San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Chemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

* To whom correspondence should be addressed.
Chittibabu Guda, E-mail: cguda{at}albany.edu


  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 9 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, 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.

Supplementary data: Accessible as online-only from the publisher.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief Funct Genomic ProteomicHome page
R. Casadio, P. L. Martelli, and A. Pierleoni
The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation
Brief Funct Genomic Proteomic, February 18, 2008; (2008) eln003v1.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
S. Schmidt von Braun, A. Sabetti, P. J. Hanic-Joyce, J. Gu, E. Schleiff, and P. B. M. Joyce
Dual targeting of the tRNA nucleotidyltransferase in plants: not just the signal
J. Exp. Bot., December 1, 2007; 58(15-16): 4083 - 4093.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Pierleoni, P. L. Martelli, P. Fariselli, and R. Casadio
eSLDB: eukaryotic subcellular localization database
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D208 - D212.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Guda
pTARGET: a web server for predicting protein subcellular localization.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W210 - W213.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.