Introduction

gkm-SVM is a sequence-based method for predicting and detecting the regulatory vocabulary encoded in functional DNA elements, and is a commonly used tool for studying gene regulatory mechanisms. Here we introduce new software, LS-GKM, which removes several limitations of our previous releases, enabling training on much larger scale (LS) datasets. LS-GKM also provides additional advanced gapped k-mer based kernel functions. With these improvements, LS-GKM achieves considerably higher accuracy than the original gkm-SVM.C/C ++ source codes and related scripts are freely available from http://github.com/Dongwon-Lee/lsgkm/, and supported on Linux and Mac OS X.dwlee@jhu.eduSupplementary data are available at Bioinformatics online.

Publications

  1. LS-GKM: a new gkm-SVM for large-scale datasets.
    Cite this
    Lee D, 2016-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Dongwon Lee
    Investigator

    McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, United States of America

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Summary
AccessionBT005121
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByDongwon Lee