GkmSVM: an R package for gapped-kmer SVM.

ABSTRACT:

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

[e-mail] or [e-mail]

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Ghandi M 

PROVIDER: S-EPMC4937197 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature