DNase-Seq
DNase-seq (
DNase-seq Footprinting
DNase-seq requires some downstream bioinformatics analyses in order to provide genome-wide DNA footprints. The computational tools proposed can be categorized in two classes: segmentation-based and site-centric approaches. Segmentation-based methods are based on the application of Hidden Markov models or sliding window methods to segment the genome into open/closed chromatin region. Examples of such methods are: HINT,[5] Boyle method[6] and Neph method.[7] Site-centric methods, on the other hand, find footprints given the open chromatin profile around motif-predicted binding sites, i.e., regulatory regions predicted using DNA-protein sequence information (encoded in structures such as Position weight matrix). Examples of these methods are CENTIPEDE[8] and Cuellar-Partida method.[9]
References
External links
- DNase I footprinting analysis of DNase-seq data in R/Bioconductor
- HINT : Tutorial for detection of DNAse footprints with HINT.
- CENTIPEDE Website