EpiSAFARI

EpiSAFARI is a computational tool to detect valley patterns in genomewide signal profiles generated from functional genomics experiments such as ChIP-Seq and bisulfite sequencing. These valley patterns are indicative of cis-regulatory elements like enhancers and insulators. EpiSAFARI employs a novel smoothing method to reduce noise in the signal profiles while accounting for technical factors such as sparse signals, mappability, and nucleotide content.
The histone modification and DNA methylation valleys detected by EpiSAFARI exhibit high conservation, transcription factor binding, and enrichment in nascent transcription, suggesting their functional significance in gene regulation and chromatin structure.