Classification performance of the SVM based on nucleosome positioning information model for five organisms.

<p>Values in parentheses indicate the area under the receiver operating characteristic curve (AUC) for each organism.</p

Model-specific values of accuracy.

<p>The accuracy values is plotted for each model. The bars indicate the measured accuracy value. (a) Accuracy values using the map1 as the reference. (b) Accuracy values using the map2 as the reference.</p

Detailed view of the predictions of intrinsic nucleosome organization along GAL1-10 locus (Chromosome II: 276930-279990) and comparison to Segal's and Yuan's results.

<p>The first top two line are nucleosome occupancy profile predicted by our model and Segal's. The black boxes in the third, fourth and fifth line are the identified nucleosome positions in this study, Yuan (N-score) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109395#pone.0109395-Yuan2" target="_blank">[6]</a> and Segal et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109395#pone.0109395-Segal1" target="_blank">[5]</a>, respectively.</p

AUC values of our model compared with previous work.

<p>AUC values of our model compared with previous work.</p

Comparisons of four methods (Our method, Reference method A, Reference method B, Reference method C) across five organisms.

<p>The point represents corresponding correlation coefficients between each vector component and nucleosome occupancy.</p

The average nucleosome occupancy predicted by our model compared with some experimental results for a typical 20,000-bp-long genomic region.

<p>The top line represents the average nucleosome occupancy predictions from our model. The second graph represents the experimental map in vitro. The third, fourth and fifth graphs represent in vivo experimental maps for three growth conditions (YPD, galactose and ethanol), respectively.</p

The correlation coefficient between cross-platform nucleosome positioning along Chromosome III.

<p>In the heat maps, the marked number represents corresponding correlation coefficients between datasets.</p

Summary of experimental methods.

<p>Summary of experimental methods.</p

Graphic illustration of the correlation of each of the twelve structural features with index-vector (Sequence data is the synthetic 150-mer nucleosome occupancy data measured by microarray from Kaplan et al. [9]).

<p>Graphic illustration of the correlation of each of the twelve structural features with index-vector (Sequence data is the synthetic 150-mer nucleosome occupancy data measured by microarray from Kaplan et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109395#pone.0109395-Kaplan1" target="_blank">[9]</a>).</p

The number of predicted nucleosomes across six maps (This study, Yuan(N-score), Albert(H2A.Z), Mavrich(H3/H4), Segal(0.5), Segal(0.2)) along Chromosome III.

<p>The number of predicted nucleosomes across six maps (This study, Yuan(N-score), Albert(H2A.Z), Mavrich(H3/H4), Segal(0.5), Segal(0.2)) along Chromosome III.</p