Figure 5.

REPARATION assisted reannotation of bacterial genomes. The figures depict the Ribo-seq and RNA-seq profiles of the ORFs with the x-axis representing the nucleotide positions. Features of reading frames are depicted as ORF plots in the upper panel, here all potential start (green (ATG) and blue (TTG, GTG)) and stop (red) codons are indicated as vertical bars across all three reading frames. (A) REPARATION predicted an in-frame 5′ extension of the adhP gene (Salmonella) with supportive N-terminal peptide data. (B) Gene yidR (Escherichia coli) predicted as a 5′ truncation with N-terminal peptide support and Ribo-seq reads starting downstream of the annotated start. (C) Novel putative coding intergenic ORF in the region Chromosome: 2 819 729-2 820 325 (Salmonella) with supportive peptide evidence. (D) Evidence of translation within pseudogene sugR (Salmonella), with three matching peptide identifications.