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. 2023 Feb 2;51(5):2377–2396. doi: 10.1093/nar/gkad040

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© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 3. — Effect of different sequence parameters on translation initiation in Lib_random. (A) Correlation of GC-content and different mRNA folding metrics with rTR. Spearman's ρ² and Pearson's R² are displayed. (B) Scatterplot between rTR and the best-correlating mRNA folding parameter efeC. (C) Correlation of rTR with local mRNA accessibility. Parameters accT_10nt and accC_10nt correspond to the mRNA accessibility of a 10-nt window centred around the mRNA position specified on the horizontal axis. Endings C and T denote base pairing calculated by two different energy models (Methods). (D) Correlation of hybridisation energy between 16S rRNA and different mRNA positions with rTR. Positional hybridisation energy (hyb_pos) is displayed for 9-bp windows centred around the indicated mRNA position (horizontal axis). (E) Relative feature importance of a random forest model trained on Lib_random. The ten most important of 248 features are displayed. hyb_opt: best-correlating hybridisation parameter (see main text). accC_{1nt, pos+6}: accC score for position +6 of the mRNA. U_{pos –1}: one-hot encoded U at position −1 of the mRNA. (F) Mean rTR of variants in Lib_random as grouped by the two most predictive features of the random forest, hyb_opt and efeC. Tick labels mark the boundaries of the respective bins (boxes).