riboviz: analysis and visualization of ribosome profiling datasets

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...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 18; no. 1; pp. 461 - 4
Main Authors: Carja, Oana, Xing, Tongji, Wallace, Edward W. J., Plotkin, Joshua B., Shah, Premal
Format: Journal Article
Language:English
Published: London BioMed Central 25.10.2017
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Algorithms
Applications programs
Bias
Bioinformatics
Biomedical and Life Sciences
Computation
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer applications
Data processing
Datasets
Diagnosis
Exploration
Footprints
Gene expression
Gene regulation
Genomes
Life Sciences
Microarrays
Next-generation sequencing
Pipelines
Protein biosynthesis
Protein synthesis
Proteins
Researchers
Ribosome profiling
Ribosomes
Sequence analysis (applications)
Source code
Stem cells
Transcription
Transcription (Genetics)
Translation quantification
Visualization
Visualization (Computer)
Visualization and comparison tool-kit
Yeast
Database
Translation quantification
Visualization and comparison tool-kit
Ribosome profiling
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Description
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riboviz consists of a comprehensive and flexible computational pipeline that allows the user to analyze private, unpublished datasets, along with a web application for comparison with published yeast datasets.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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-017-1873-8