Genomic Analysis Using Short Sequencing Tags

Abstract

ChIP-seq is a revolutionary assay used to detect the binding sites of TF in the entire genome, made possible through the rapid advancement in high-throughput sequencing technology. The precision of the binding location of TF can be detected within positional accuracy of +/-200 bp. Motif predictions of TF binding sites tend to yield a much greater accuracy when restricted to regions near ChIP-seq peaks. This thesis studies the problems related to prediction of cofactors by taking advantage of the high resolution of the technology.