1. Mononucleotide models describe sequence‐to‐shape relationships well
Mononucleotide models describe sequence‐to‐shape relationships well Schematic diagram showing how pentamer tables currently are used to evaluate the DNA shape parameters and how we alternatively evaluate them using sequence feature‐based models.Fraction of variance explained (R2) for models with mononucleotide predictors only (green) and models with mono‐ and dinucleotide predictors (increase shown in blue). Leave‐one‐out cross‐validation was used.Scatter plots of true vs. predicted shape parameters. Green dots indicate predictions by the mononucleotide models, whereas blue dots indicate predictions by models that also include dinucleotide interactions.Regression coefficients of mononucleotide‐only sequence‐to‐shape models, shown as logos. The models were trained on the shape pentamer tables of Zhou et al (2013). B0 and P0 indicate the positions of the central base and base pair step, respectively.Regression coefficients for an all‐by‐all interaction model (red, above average; blue, below). Diagonal blocks indicate self‐interactions (equivalent to mononucleotide‐based predictors), and off‐diagonal blocks indicate interactions.Logo representation of dinucleotide interactions using the representation in (D). Dashed lines separate columns of dinucleotides.
H Tomas Rube et al. Mol Syst Biol 2018;14:e7902
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