Computational resources for ribosome profiling: from database to Web server and software

@article{Wang2019ComputationalRF,
  title={Computational resources for ribosome profiling: from database to Web server and software},
  author={Hongwei Wang and Yan Wang and Zhi Xie},
  journal={Briefings in Bioinformatics},
  year={2019},
  volume={20},
  pages={144–155}
}
Abstract Ribosome profiling is emerging as a powerful technique that enables genome‐wide investigation of in vivo translation at sub‐codon resolution. The increasing application of ribosome profiling in recent years has achieved remarkable progress toward understanding the composition, regulation and mechanism of translation. This benefits from not only the awesome power of ribosome profiling but also an extensive range of computational resources available for ribosome profiling. At present… 

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References

SHOWING 1-10 OF 72 REFERENCES
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
TLDR
A ribosomesome-profiling strategy based on the deep sequencing of ribosome-protected mRNA fragments is presented and enables genome-wide investigation of translation with subcodon resolution and is used to monitor translation in budding yeast under both rich and starvation conditions.
Ribosome profiling: new views of translation, from single codons to genome scale
TLDR
It is shown that ribosome profiling is an emerging technique that uses deep sequencing to monitor in vivo translation and provides new insights into the identity and the amount of proteins that are produced by cells, as well as detailed views into the mechanism of protein synthesis itself.
Ribosome profiling reveals the what, when, where and how of protein synthesis
TLDR
The methodology of ribosome profiling is introduced and examples in which this approach has been a key factor in guiding biological discovery, including its prominent role in identifying thousands of novel translated short open reading frames and alternative translation products are discussed.
The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.
TLDR
A modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility is described, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination.
PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
TLDR
The PROTEOFORMER tool is developed, which automatically processes data of the recently developed ribosome profiling method, resulting in genome-wide visualization of Ribosome occupancy, and enables proteome-wide detection of 5′-extended proteoforms, upstream ORF translation and near-cognate translation start sites.
Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data
TLDR
Results indicate that the tRNA pool adaptation hypothesis is incomplete, with evidence suggesting that tRNA post-transcriptional modifications and codon context may play a role in determining codon elongation rates.
sORFs.org: a repository of small ORFs identified by ribosome profiling
TLDR
SORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects, and incorporates state-of-the-art tools and metrics.
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
TLDR
An adaptation that reveals the sites of translation initiation by pretreating cells with harringtonine to immobilize initiating ribosomes is described, paving the way for genome-wide, quantitative analysis of in vivo translation by deep sequencing.
Insights into the mechanisms of eukaryotic translation gained with ribosome profiling
TLDR
This review will focus on how recent findings made with RiboSeq have revealed important details of the molecular mechanisms of translation in eukaryotes.
...
...