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. 2022 Jan 17;23(2):bbab549. doi: 10.1093/bib/bbab549

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© The Author(s) 2022. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Comparison of manual Ribo-seq curation, proteomics data, and tool performance for representative E. coli genes. for the translatome sets of the four organisms. Highly conserved and translated long ribosomal protein operon between rpmJ and secY, including several essential sORFs. Related to Supplemental Figure S4. (B) The highly conserved Gammaproteobacteria cydABX operon in E. coli. The final gene in the operon, cydX, encodes a functional small protein [81]. Related to Supplemental Figure S2. The space between cydA and cydB is 15 nt. (C) The ORF encoding the small protein AcrZ, an antibiotic efflux pump specificity factor [82, 83]. For all screenshots, genes that are detected in the publicly available proteomics (MS) dataset and by manual curation of the Ribo-seq data (label) are indicated in dark gray. Detection by the indicated tools at a 70% overlap threshold is indicated in gray based on Ribo-seq data (or RNA-seq, IRSOM). Those that are not detected as translated are white. Transcriptional start sites, if available, are indicated with a bent arrow ().

Inline graphic — Comparison of manual Ribo-seq curation, proteomics data, and tool performance for representative E. coli genes. for the translatome sets of the four organisms. Highly conserved and translated long ribosomal protein operon between rpmJ and secY, including several essential sORFs. Related to Supplemental Figure S4. (B) The highly conserved Gammaproteobacteria cydABX operon in E. coli. The final gene in the operon, cydX, encodes a functional small protein [81]. Related to Supplemental Figure S2. The space between cydA and cydB is 15 nt. (C) The ORF encoding the small protein AcrZ, an antibiotic efflux pump specificity factor [82, 83]. For all screenshots, genes that are detected in the publicly available proteomics (MS) dataset and by manual curation of the Ribo-seq data (label) are indicated in dark gray. Detection by the indicated tools at a 70% overlap threshold is indicated in gray based on Ribo-seq data (or RNA-seq, IRSOM). Those that are not detected as translated are white. Transcriptional start sites, if available, are indicated with a bent arrow ().