Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events

Nucleic Acids Res. 2018 Oct 12;46(18):e109. doi: 10.1093/nar/gky533.


Translation is dynamically regulated during cell development and stress response. In order to detect actively translated open reading frames (ORFs) and dynamic cellular translation events, we have developed a computational method, RiboWave, to process ribosome profiling data. RiboWave utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes and precisely locate their footprint denoted as Periodic Footprint P-site (PF P-site). Such high-resolution footprint is found to capture the full track of actively elongating ribosomes, from which translational landscape can be explicitly characterized. We compare RiboWave with several published methods, like RiboTaper, ORFscore and RibORF, and found that RiboWave outperforms them in both accuracy and usage when defining actively translated ORFs. Moreover, we show that PF P-site derived by RiboWave shows superior performance in characterizing the dynamics and complexity of cellular translatome by accurately estimating the abundance of protein levels, assessing differential translation and identifying dynamic translation frameshift.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arabidopsis
  • Cells, Cultured
  • Computational Biology / methods*
  • HCT116 Cells
  • Humans
  • Mice
  • Open Reading Frames
  • Peptide Chain Elongation, Translational*
  • Polyribosomes / metabolism
  • Protein Biosynthesis
  • Protein Footprinting / methods*
  • RNA, Messenger / metabolism
  • Ribosomes / metabolism*
  • Signal-To-Noise Ratio
  • Systems Analysis
  • Wavelet Analysis


  • RNA, Messenger