RT Journal Article
SR Electronic
T1 riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 169862
DO 10.1101/169862
A1 Fabio Lauria
A1 Toma Tebaldi
A1 Paola Bernabò
A1 Ewout J.N. Groen
A1 Thomas H. Gillingwater
A1 Gabriella Viero
YR 2017
UL http://biorxiv.org/content/early/2017/07/28/169862.abstract
AB 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 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 data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies.Availability and Implementation riboWaltz was implemented in R and is available at https://github.com/LabTranslationalArchitectomics/RiboWaltzContact gabriella.viero{at}cnr.it or fabio.lauria{at}unitn.it