gkmSVM：一个用于带间隔k-mer支持向量机的R软件包。
gkmSVM: an R package for gapped-kmer SVM.
作者信息
Ghandi Mahmoud, Mohammad-Noori Morteza, Ghareghani Narges, Lee Dongwon, Garraway Levi, Beer Michael A
机构信息
The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran.
出版信息
Bioinformatics. 2016 Jul 15;32(14):2205-7. doi: 10.1093/bioinformatics/btw203. Epub 2016 Apr 19.
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.
摘要
未标注
我们展示了一个新的R包，用于训练针对DNA和蛋白质序列的带间隙k-mer支持向量机（SVM）分类器。我们描述了一种改进的核矩阵计算算法，其运行时间比我们原来的gkmSVM算法快约2至5倍。该包支持多种序列核，包括：gkmSVM、kmer-SVM、错配核和通配符核。
可用性与实现
gkmSVM包可通过综合R存档网络（CRAN）免费获取，适用于Linux、Mac OS和Windows平台。C++实现可在www.beerlab.org/gkmsvm获取。
联系方式
mghandi@gmail.com或mbeer@jhu.edu
补充信息
补充数据可在《生物信息学》在线获取。
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