Carja Oana, Xing Tongji, Wallace Edward W J, Plotkin Joshua B, Shah Premal
Department of Biology, University of Pennsylvania, 204K Lynch Labs, 433 S University Ave, Philadelphia, 19104, PA, USA.
Department of Genetics, Rutgers University, Piscataway, NJ, USA.
BMC Bioinformatics. 2017 Oct 25;18(1):461. doi: 10.1186/s12859-017-1873-8.
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.
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riboviz consists of a comprehensive and flexible computational pipeline that allows the user to analyze private, unpublished datasets, along with a web application for comparison with published yeast datasets.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.
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.
核糖体分析利用高通量测序技术在体内监测翻译过程，能够为深入了解细胞内蛋白质合成的动态变化及调控机制提供关键信息。自2009年该技术问世以来，它在推动生物学发现方面发挥了关键作用，但要广泛应用还需要一套严谨的计算工具包。
我们开发了一个数据库以及基于浏览器的可视化工具riboviz，用于探索和分析核糖体测序数据集。在实际应用中，riboviz包含一个全面且灵活的计算流程，允许用户分析私人的、未发表的数据集，同时还提供一个网络应用程序，用于与已发表的酵母数据集进行比较。源代码和详细文档可从https://github.com/shahpr/RiboViz免费获取。网络应用程序可在www.riboviz.org上使用。
riboviz提供了一个全面的数据库以及分析和可视化工具，用于对核糖体分析数据集进行比较分析。该工具包将有助于研究全基因组核糖体分析数据的系统生物学界，以及专注于单个基因的研究小组识别不同生物体和条件下转录和翻译调控的模式。
