Identification of optimal motif length using the <i>NNAlign</i> method.

Abstract

<p><b>Left panel:</b> Histogram of the optimal motifs lengths for the 14 HLA-DR molecules in the Wang dataset as identified by the <i>NNAlign</i> method. Right panel: Predictive performance measured in terms of the root mean square error (RMSE) between observed and predicted values as a function of the motif length for the two molecules DRB1*0101 and DRB1*1501. <i>NNAlign</i> was trained using the same parameters settings described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026781#pone-0026781-g004" target="_blank">Figure 4</a>. At each motif length are shown the mean and standard error of the mean RMSE as estimated by bootstrap sampling. For DRB1*0101 a single consistent optimal motif length of 9 amino acids is found. For DRB1*1501 all motif length 8–11 had statistically indistinguishable performance (paired t-test).</p