Finding the Needle in the Haystack: Computational Strategies for Discovering Regulatory Sequences in Genomes

Annotating the noncoding portion of the human genome and identifying functional regulatory elements embedded in its sequence creates a continuing challenge. Historically, the functional characterization of regulatory elements has been slow, labor-intensive and inadequate to keep up with the demands of whole-genome analysis. Recently, there has been an explosion of computational techniques and tools available to assist in the annotation of noncoding DNA and improve the accurate prediction of regulatory sequences. Here, we review some of the bioinformatic strategies and computational tools that are increasingly being used to analyze large genomic data sets and to facilitate the high-throughput identification of candidate regulatory sequences in whole genomes.