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Figure 2 | BMC Bioinformatics

Figure 2

From: Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning

Figure 2

The effect of TIS orientation on the PAS method and the LS method and selection of the data for performance comparison. A. A schematic representation illustrating the difference in probabilities of initiation (Pi) estimated using the PAS method (equation (1), red) and the LS method (equation (4), blue). B. The frequency of each codon as the first or the last TIS in an mRNA. The distributions were generated using mRNAs with multiple starts from Ingolia et al. [3] data. C. The barcharts indicate the number of mRNAs with a varying number of TISs (1 to 6) for genes encoding a single transcript isoform from each dataset (Lee et al. [4] (blue Human, red Mouse) and Ingolia et al. [3] (green Mouse)). The pie charts show the relative frequency of two TISs transcripts containing three different configurations of TIS ORFs: TISs that belong to overlapping ORFs (top), TISs that belong to the same ORF (middle right) and TISs that belong to ORFs separated by a non-translated region (bottom). D. The frequencies of non-AUG codons among all TISs (top bars) and in 5′ leaders, i.e. upstream of annotated TISs, (middle bars) in the 2 TISs mRNA datasets selected for testing the PAS and LS methods. The bottom bars “# Footprints” represent the proportion of footprint reads detected at all non-AUG TISs.

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BMC Bioinformatics

ISSN: 1471-2105

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