gkmSVM: an R package for gapped-kmer SVM

Bioinformatics. 2016 Jul 15;32(14):2205-7. doi: 10.1093/bioinformatics/btw203. Epub 2016 Apr 19.


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: mghandi@gmail.com or mbeer@jhu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Algorithms
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, Protein / methods*
  • Software*
  • Support Vector Machine*