We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorithm. This package supports several sequence kernels, includin...
Sequence analysisgkmSVM: an R package for gapped-kmer SVMMahmoud Ghandi 1, *, Morteza Mohammad-Noori 2 ,Narges Ghareghani 3 , Dongwon Lee 4 , Levi Garraway 1,5 andMichael A. Beer 4,6, *1 The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 2 School of Mathematics, ...