svmPRAT is a general purpose protein residue annotation toolkit to allow biologists to formulate residue-wise prediction problems. svmPRAT formulates annotation problem as a classification or regression problem using support vector machines. The key features of svmPRAT are its ease of use to incorporate any user-provided information in the form of feature matrices. For every residue svmPRAT captures local information around the reside to create fixed length feature vectors. svmPRAT implements accurate and fast kernel functions, and also introduces a flexible window-based encoding scheme that allows better capture of signals for certain prediction problems.
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BMC Bioinformatics. 2009 Dec 22;10:439.
svmPRAT: SVM-based protein residue annotation toolkit.
Rangwala H, Kauffman C, Karypis G.