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

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/.