Estimating the statistical significance of sequence motifs

The identification of transcription factor binding sites is an important step in understanding the regulation of gene expression. To address this need, many motif-finding tools have been described that can find short sequence motifs given only an input set of sequences.

Somewhat surprisingly, development of the significance analysis of the motifs reported by those motif finders has lagged considerably behind the extensive development of the finders themselves. Nevertheless, this analysis is often crucial in helping scientists decide whether or not to carry the predicted motifs to the next stage of their analysis. We will discuss the problem of evaluating the statistical significance of sequence motifs in the general context of evaluating the statistical significance of an observed result.

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