Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae

Motivation: We demonstrate a computational process by which transcription factor binding sites can be elucidated using genome-wide expression and binding profiles. The profiles direct us to the intergenic locations likely to contain the promoter regions for a given factor. These sequences are multiply and locally aligned to give an anchor motif from which further characterization can take place. Results: We present bases for and assumptions about the variability within these motifs which give rise to potentially more accurate motifs, capture complex binding sites built upon the basis motif, and eliminate the constraints of the currently employed promoter searching protocols. We also present a measure of motif quality based on the occurrence of the putative motifs in regions observed to contain the binding sites. The assumptions, motif generation, quality assessment and comparison allow the user as much control as their a priori knowledge allows.