Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns.

ABSTRACT: Non-methylated islands (NMIs) of DNA are genomic regions that are important for gene regulation and development. A recent study of genome-wide non-methylation data in vertebrates by Long et al. (eLife 2013;2:e00348) has shown that many experimentally identified non-methylated regions do not overlap with classically defined CpG islands which are computationally predicted using simple DNA sequence features. This is especially true in cold-blooded vertebrates such as Danio rerio (zebrafish). In order to investigate how predictive DNA sequence is of a region's methylation status, we applied a supervised learning approach using a spectrum kernel support vector machine, to see if a more complex model and supervised learning can be used to improve non-methylated island prediction and to understan

SUBMITTER: Huska M 

PROVIDER: S-EPMC5161304 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature