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Nucleic Acids Research 2006 34(Web Server issue):W210-W213; doi:10.1093/nar/gkl093
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

pTARGET: a web server for predicting protein subcellular localization

Chittibabu Guda

Gen*NY*sis Center for Excellence in Cancer Genomics and Department of Epidemiology and Biostatistics, University at Albany, State University of New York 1 Discovery drive, Rensselaer, NY 12144-3456, USA

To whom correspondence should be addressed. Tel: +1 518 591 7155; Fax: +1 518 591 7151; Email: cguda{at}albany.edu

Received February 6, 2006. Revised February 18, 2006. Accepted March 7, 2006.

The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963–3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770 000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from http://bioinformatics.albany.edu/~ptarget.


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