Model | Summary | Performance (Pearson R) | Correlation with %G+C (Yeast, 150 bp windows) | |||||
---|---|---|---|---|---|---|---|---|
 |  | Synthetic oligonucleotides (Microarray)[8] | Synthetic oligonucleotides (Sequencing)[8] | Yeast in vitro[8] | Yeast in vivo[2] | C. elegans adjusted nucleosome coverage[34] | C. elegans normalized occupancy[34] |  |
Kaplan et al., 2009[8] | Probabilistic model based on in vitro 5-mer preferences and periodic dinucleotide signal. | 0.51* | 0.45* | 0.89* | 0.34 | 0.47* | 0.61* | 0.87 |
Lasso model (this study) | See Methods. | 0.44 | 0.41 | 0.86* | 0.38* | 0.49* | 0.66* | 0.85 |
Field et al., 2008[24] | Probabilistic model based on 5-mer preferences measured in vivo (yeast) and periodic dinucleotide signals. | 0.47* | 0.45* | 0.74 | 0.39* | 0.46* | 0.61* | 0.64 |
%G+C | The percentage of guanine and cytosine bases in a DNA sequence. | 0.53* | 0.49* | 0.78* | 0.25 | 0.42 | 0.47 | 1 |
Lasso model[2] | Linear regression model trained on in vivo nucleosome occupancy data. Uses DNA structural parameters, excluding sequences and transcription factor binding sites (ABF1, REB1, and STB2) as inputs. | 0.23 | 0.22 | 0.63 | 0.45* | 0.38 | 0.5 | 0.55 |
Peckham et al., 2007[25] | SVM classifier trained on overrepresented k-mers (k = 1-6) found in nucleosome occupied and depleted sequences determined in vivo yeast data. | 0.43 | 0.39 | 0.48 | 0.22 | 0.29 | 0.33 | 0.57 |
Yuan and Liu, 2008[26] | Computes predicted nucleosome occupancy based on periodic dinucleotide signals found in nucleosomal and linker DNA sequences determined from in vitro and in vivo experiments in yeast | 0.02 | 0.05 | 0.35 | 0.27 | 0.36 | 0.48 | 0.30 |
Miele et al., 2008[29] | Computes free energy landscape of nucleosome formation using an estimation of dinucleotide-dependent DNA flexibility and intrinsic curvature. | 0.32 | 0.26 | 0.38 | 0.22 | 0.21 | 0.25 | 0.49 |
Segal et al., 2006[23] Downloaded January 2007 | Probabilistic model trained on yeast data, using a position specific scoring matrix derived from a collection of nucleosome-bound sequences obtained from in vitro selection experiments. | NaN | NaN | 0.05 | 0.09 | 0.05 | 0.05 | 0.07 |
Ioshikhes et al., 2006[22] | Computes the correlation of periodic AA/TT dinucleotide motifs in a given sequence with those found in a set of 204 eukaryotic and viral nucleosomal sequences determined through in vivo and in vitro experiments[20]. | -0.03 | -0.03 | 0.01 | 0.07 | -0.03 | -0.01 | 0.01 |
Estimates the dinucleotide-dependent cost of deformation caused by threading a given sequence on a template comprising the path of DNA found on the experimentally determined structure of the nucleosome core particle. | 0.01 | 0.004 | 0 | -0.001 | -0.001 | -0.001 | -0.0003 | |
Segal et al., 2006[23] Downloaded August 2009 | Probabilistic model trained on yeast data, using a position specific scoring matrix derived from a collection of nucleosome-bound sequences obtained from in vitro selection experiments. | NaN | NaN | -0.2 | 0.001 | -0.06 | -0.05 | -0.21 |