CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.

ABSTRACT: High-throughput bisulfite sequencing is widely used to measure cytosine methylation at single-base resolution in eukaryotes. It permits systems-level analysis of genomic methylation patterns associated with gene expression and chromatin structure. However, methods for large-scale identification of methylation patterns from bisulfite sequencing are lacking. We developed a comprehensive tool, CpG_MPs, for identification and analysis of the methylation patterns of genomic regions from bisulfite sequencing data. CpG_MPs first normalizes bisulfite sequencing reads into methylation level of CpGs. Then it identifies unmethylated and methylated regions using the methylation status of neighboring CpGs by hotspot extension algorithm without knowledge of pre-defined regions. Furthermore, the conserva

SUBMITTER: Su J 

PROVIDER: S-EPMC3592415 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature