riboviz: analysis and visualization of ribosome profiling datasets.

Carja O and Xing T and Wallace EWJ and Plotkin JB and Shah P, BMC Bioinformatics 18 (1) :461 (2017).

Summary

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riboviz consists of a comprehensive and flexible computational pipeline that allows the user to analyze private, unpublished datasets, along with a web application for comparison with published yeast datasets.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: Ribosome profiling, Translation quantification, Database, Visualization and comparison tool-kit