DNA Sequence Motif: A Jack of All Trades for ChIP-Seq Data

摘要: Nowadays, chromatin immunoprecipitation followed by next-generation sequencing, often referred to as ChIP-Seq, has become an industry standard study a landscape of DNA-protein interactions in vivo. ChIP-Seq captures highly specific protein-DNA interactions, such transcription factors (TFs) bound appropriate binding sites, and sparse patterns formed different histone marks. In this review, we focus on DNA sequence analysis methods adequate for TF data. We discuss numerous tasks starting from basic motif finding discovery is, further applied explore various features experimental show how data derives novel biological knowledge multiple levels, individual factor sites genome segments operating regulatory modules. Finally, provide overview existing software the field.