gkmSVM: an R package for gapped-kmer SVM.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 27153639.
- Also identified by DOI 10.1093/bioinformatics/btw203 and PMC identifier 4937197.
- No licence information is recorded for this record.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
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. 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 mghandi@gmail.com or mbeer@jhu.edu Supplementary data are available at Bioinformatics online.
Medical subject headings
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Software
- Support Vector Machine