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.
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Acknowledgments
This work supported by Deutsche Forschungsgemeinschaft (grant TR175) and the Federal Ministry for Education and Research (BMBF, grant de.NBI/RBC). The authors acknowledge helpful feedback and support from Antje Hirsekorn and Dilmurat Yusuf.
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Harnett, D., Meerdink, E., Calviello, L., Sydow, D., Ohler, U. (2021). Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant. In: Labunskyy, V.M. (eds) Ribosome Profiling. Methods in Molecular Biology, vol 2252. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1150-0_16
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DOI: https://doi.org/10.1007/978-1-0716-1150-0_16
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