riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

113Citations
Citations of this article
142Readers
Mendeley users who have this article in their library.

Abstract

Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine the trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies. riboWaltz was implemented in R and is available as an R package at https://github.com/LabTranslationalArchitectomics/RiboWaltz.

Cite

CITATION STYLE

APA

Lauria, F., Tebaldi, T., Bernabò, P., Groen, E. J. N., Gillingwater, T. H., & Viero, G. (2018). riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. PLoS Computational Biology, 14(8). https://doi.org/10.1371/journal.pcbi.1006169

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free