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Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
gkmSVM: an R package for gapped-kmer SVM.
Bioinformatics 2016 July 16
UNLABELLED: 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, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.
AVAILABILITY AND IMPLEMENTATION: gkmSVM package is freely available through the Comprehensive R Archive Network (CRAN), for Linux, Mac OS and Windows platforms. The C ++ implementation is available at www.beerlab.org/gkmsvm
CONTACT: [email protected] or [email protected]
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
AVAILABILITY AND IMPLEMENTATION: gkmSVM package is freely available through the Comprehensive R Archive Network (CRAN), for Linux, Mac OS and Windows platforms. The C ++ implementation is available at www.beerlab.org/gkmsvm
CONTACT: [email protected] or [email protected]
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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