Journal
BIOINFORMATICS
Volume 32, Issue 14, Pages 2205-2207Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btw203
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Funding
- NIH [R01 HG0007348]
- IPM [CS1391-4-02, 94050016]
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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
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