Mnt binding matrices.

<p>A. The experimentally observed relative frequency of each type of DNA base at each position in the 7-long Mnt protein half-site. The highest affinity site is: 5′-GTGGACC-3′. B. The negative log2 of the values shown in A. Each entry represents the binding energy contributed by a particular base at that position in the site to the total binding energy. This matrix represents the “true” binding model.</p

Creating a ROC curve.

<p>This figure shows a portion of a typical spreadsheet used to construct a ROC curve. In this example the PWM model is a log-odds model based on 50 sites. The cutoff is 4 and the sampling mode is Boltzmann. There are 77 sites whose true energy is below or equal to the cutoff (i.e. K = 77). In the original spreadsheet the index <i>i</i> runs from 1 to 16,384.</p

Receiver operator characteristic curves of the position weight matrix models with step-function sampling.

<p>The log-odds, Match, and quadratic programming results are denoted by red, yellow, and blue markers respectively. Each data point is the mean of five replicates and points are allowed to overlap. Error as standard deviation of the mean extends from each curve by the size of a single marker. A. Alignments containing 20 sites; cutoff = 4. The log-odds, Match, and quadratic programming curves attain TP = 1 at FP = 0.013, 0.099, and 0.019, respectively. B. Alignments containing 20 sites; cutoff = 7. The log-odds, Match, and quadratic programming curves attain TP = 1 at FP = 0.329, 0.495, and 0.200, respectively. C. Alignments containing 50 sites; cutoff = 4. The log-odds, Match, and quadratic programming curves attain TP = 1 at FP = 0.014, 0.057, and 0.011, respectively. D. Alignments containing 50 sites; cutoff = 7. The log-odds, Match, and quadratic programming curves attain TP = 1 at FP = 0.151, 0.437, and 0.070, respectively. E. Alignments containing 200 sites; cutoff = 4. The log-odds, Match, and quadratic programming curves attain TP = 1 at FP = 0.009, 0.038, and 0.006, respectively. F. Alignments containing 200 sites; cutoff = 7. The log-odds, Match, and quadratic programming curves attain TP = 1 at FP = 0.061, 0.253, and 0.013, respectively.</p

The log2 of the number of sequences in the population of all DNA 7-mers that are below or equal to the relative binding energy indicated on the x-axis.

<p>The “log2 of cutoff” is a DNA-protein binding energy based on the affinity values listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006736#pone-0006736-g001" target="_blank">Figure 1B</a>.</p

Performance of the position weight matrix models with Boltzmann sampling.

<p>A–C. Alignments containing 20 sites. D–F. Alignments containing 50 sites. G–I. Alignments containing 200 sites. The log-odds, Match, and quadratic programming results are denoted by the red open-square, yellow open-diamond, and blue filled-oval markers respectively. Each data point is the mean of five replicates. Error bars denote the standard deviation of the mean.</p

Performance of the position weight matrix models with step-function sampling.

<p>A–C. Alignments containing 20 sites. D–F. Alignments containing 50 sites. G–I. Alignments containing 200 sites. The log-odds, Match, and quadratic programming results are denoted by the red open-square, yellow open-diamond, and blue filled-oval markers respectively. Each data point is the mean of five replicates. Error bars denote the standard deviation of the mean.</p