QuEST

QuEST is a software tool that uses a kernel density estimator-based package to identify molecular interactions between protein complexes and DNA. It is particularly useful for uncovering such interactions by chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq), which has recently become the focus of intense interest.

What makes QuEST powerful is its statistical framework based on the kernel density estimation approach, which uses ChIP-Seq data to determine positions where protein complexes contact DNA. This enables the discovery of thousands of binding sites for human transcription factors, such as SRF, GABP, and NRSF, at an average resolution of about 20 base pairs.

Furthermore, QuEST allows for identifying cofactor binding specificity from ChIP-Seq data. Using MEME motif-discovery tool-based analyses of the QuEST-identified sequences, DNA binding by cofactors of SRF was revealed.

Finally, QuEST's combination with Gene Ontology (GO) annotations and expression data allows for the inference of general functions of transcription factors. This is particularly helpful when understanding how transcription factors regulate or influence gene expression.