Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines.

ABSTRACT: The chemical modification of histones at specific DNA regulatory elements is linked to the activation, inactivation and poising of genes. A number of tools exist to predict enhancers from chromatin modification maps, but their practical application is limited because they either (i) consider a smaller number of marks than those necessary to define the various enhancer classes or (ii) work with an excessive number of marks, which is experimentally unviable. We have developed a method for chromatin state detection using support vector machines in combination with genetic algorithm optimization, called ChromaGenSVM. ChromaGenSVM selects optimum combinations of specific histone epigenetic marks to predict enhancers. In an independent test, ChromaGenSVM recovered 88% of the experimentally suppo

SUBMITTER: Fernandez M 

PROVIDER: S-EPMC3378905 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature