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. 2021:2252:331-346.
doi: 10.1007/978-1-0716-1150-0_16.

Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant

Dermot Harnett  1 , Eelco Meerdink  1 , Lorenzo Calviello  2 , Dominique Sydow  1 , Uwe Ohler  3   4
Affiliations

Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant

Dermot Harnett et al. Methods Mol Biol. 2021.

Abstract

Ribosome profiling, or Ribo-seq, provides precise information about the position of actively translating ribosomes. It can be used to identify open reading frames (ORFs) that are translated in a given sample. The RiboTaper pipeline, and the ORFquant R package, leverages the periodic distribution of such ribosomes along the ORF to perform a statistically robust test for translation which is insensitive to aperiodic noise and provides a statistically robust measure of translation. In addition to accounting for complex loci with overlapping ORFs, ORFquant is also able to use Ribo-seq as a tool for distinguishing actively translated transcripts from non-translated ones, within a given gene locus.

Keywords: Genomics; Open reading frame; Periodicity; Ribo-seq; Ribosome; Sequencing; Translation.

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