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Nucleic Acids Research 2005 33(Web Server Issue):W202-W207; doi:10.1093/nar/gki587
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© The Author 2005. 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{at}oupjournals.org

Article

Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences

Manoj Bhasin and G. P. S. Raghava*

Institute of Microbial Technology Sector 39-A, Chandigarh, 160036, India

*To whom correspondence should be addressed. Tel: +91 172 2690557/2690225; Fax: +91 172 2690632/2690585; Email: raghava{at}imtech.res.in

Received November 25, 2004. Revised January 17, 2005. Accepted May 2, 2005.

This manuscript describes a support vector machine based method for the prediction of constitutive as well as immunoproteasome cleavage sites in antigenic sequences. This method achieved Matthew's correlation coefficents of 0.54 and 0.43 on in vitro and major histocompatibility complex ligand data, respectively. This shows that the performance of our method is comparable to that of the NetChop method, which is currently considered to be the best method for proteasome cleavage site prediction. Based on the method, a web server, Pcleavage, has also been developed. This server accepts protein sequences in any standard format and present results in a user-friendly format. The server is available for free use by all academic users at the URL http://www.imtech.res.in/raghava/pcleavage/ or http://bioinformatics.uams.edu/mirror/pcleavage/.


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