Dataset Information

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

mghandi@gmail.com or mbeer@jhu.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Ghandi M

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

REPOSITORIES: biostudies-literature

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Publications

gkmSVM: an R package for gapped-kmer SVM.

Ghandi Mahmoud M Mohammad-Noori Morteza M Ghareghani Narges N Lee Dongwon D Garraway Levi L Beer Michael A MA

Bioinformatics (Oxford, England) 20160419 14

<h4>Unlabelled</h4>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.<h4>Availability and implementation</h4>gkmSVM package is freely available through the Comprehensive R Archive Network (CRAN), ...[more]

PMID: 27153639