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. 2017 Oct 25;18(1):461.
doi: 10.1186/s12859-017-1873-8.

riboviz: analysis and visualization of ribosome profiling datasets

Oana Carja  1 , Tongji Xing  2 , Edward W J Wallace  3 , Joshua B Plotkin  4 , Premal Shah  5   6
Affiliations

riboviz: analysis and visualization of ribosome profiling datasets

Oana Carja et al. BMC Bioinformatics. .

Abstract

Background: Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption.

Description: We have developed a database and a browser-based visualization tool, riboviz, that enables exploration and analysis of riboseq datasets. In implementation, riboviz consists of a comprehensive and flexible computational pipeline that allows the user to analyze private, unpublished datasets, along with a web application for comparison with published yeast datasets. Source code and detailed documentation are freely available from https://github.com/shahpr/RiboViz . The web-application is live at www.riboviz.org.

Conclusions: riboviz provides a comprehensive database and analysis and visualization tool to enable comparative analyses of ribosome-profiling datasets. This toolkit will enable both the community of systems biologists who study genome-wide ribosome profiling data and also research groups focused on individual genes to identify patterns of transcriptional and translational regulation across different organisms and conditions.

Keywords: Database; Ribosome profiling; Translation quantification; Visualization and comparison tool-kit.

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Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
a The riboviz website with the user interface allowing dataset selection. b Distribution of reads mapped to YAL003W in three riboseq datasets using a Shiny web server
See this image and copyright information in PMC

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