Combinatorial control of transcription is a well established phenomenon in the cell. Multiple transcription factors often bind to the same transcriptional control region of a gene and interact with each other to control the expression of the gene. It is thus necessary to consider the joint conservation of sequence pairs in order to identify combinations of binding sites to which the transcription factors bind. Conventional motif finding algorithms fail to address this issue. We propose a novel biclustering algorithm based on random sampling to identify candidate binding site combinations. We establish bounds on the various parameters to the algorithm and study the conditions under which the algorithm is guaranteed to identify candidate binding sites. We analyzed a yeast cell cycle gene expression data set using our algorithm and recovered certain novel combinations of binding sites, besides those already reported in the literature. / Master of Science