riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data
Fig 2
(A) Distribution of the read lengths. (B) Left, percentage of P-sites in the 5’ UTR, CDS and 3’ UTR of mRNAs from ribosome profiling data. Right, percentage of region lengths in mRNAs sequences. (C) Percentage of P-sites in the three frames along the 5’ UTR, CDS and 3’ UTR, stratified for read length. (D) Example of meta-gene heatmap reporting the signal associated to the 5’ end (upper panel) and 3’ end (lower panel) of the reads aligning around the start and the stop codon for different read lengths. (E) Codon usage analysis based on in-frame P-sites. The codon usage index is calculated as the frequency of in-frame P-sites along the coding sequence associated to each codon, normalized for codon frequency in sequences. The amino-acids corresponding to the codons are displayed above each bar. All panels were obtained from ribosome profiling of whole mouse brain (GSE102318).