Open AccessgkmSVM: an R package for gapped-kmer SVM
Author(s) -
Mahmoud Ghandi,
Morteza Mohammad-Noori,
Narges Ghareghani,
Dongwon Lee,
Levi A. Garraway,
M Beer
Publication year - 2016
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btw203
Subject(s) - r package , support vector machine , computer science , artificial intelligence , pattern recognition (psychology) , data mining , programming language
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.
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