Figure 5. Differences between BSG Predictions and Gibbs Sampling.

The motif predicted by BSGs is compared with the best-scoring motif from an equivalent amount of Gibbs sampling. In some cases, such as HSF1 and LEU3, BSGs perform better through better estimation of the width of the motif. In such cases, manually choosing the correct motif width based on a priori knowledge allows Gibbs sampling to predict the correct motif. In other cases, however, such as SIP4 and RDS1, choosing the best Gibbs sampling width does not produce the correct prediction. For RDS1, N/A indicates that the motif width reported previously [29] matches the width of the best Gibbs sampling motif, and thus manually selecting the motif width does not alter the Gibbs sampling prediction.