Finding Regulatory Motifs with Maximum Density Subgraphs

The identification of over-represented but imperfectly conserved motifs in genomic DNA is a problem with important biological applications, such as the discovery of regulatory elements that determine the timing, location, and level of gene transcription. Experimental techniques such as ChIP-chip and geneexpression microarrays can identify sets of genomic regions that are likely to be enriched for binding sites of a given transcription factor, which can then be mined computationally for an associated binding motif. This problem has been tackled many times with a number of disparate methods[4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,21,29]. A thorough examination of the field has also been published [38].