A tool for analyzing and visualizing ribo-seq data at the isoform level

BMC Bioinformatics

Yan-Yuan Tseng¹  Joseph T. Tseng²  Yi-Hong Tsao²  Sheng-Cian Shiue³  Wei-Sheng Wu³  Ting-Yu Chen³ 

[1] Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, 48201, Detroit, MI, USA;Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, 701, Tainan, Taiwan;Department of Electrical Engineering, National Cheng Kung University, 701, Tainan, Taiwan;

关键词: Ribo-seq;    Ribosome profiling;    Pipeline;    Tool;    Software;    Isoform-level;    Visualization;   

DOI  :  10.1186/s12859-021-04192-7

来源: Springer

【 摘 要 】

BackgroundTranslational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo-seq, is a powerful experimental technique to study translational regulation. It can capture a snapshot of translation by deep sequencing of ribosome-protected mRNA fragments. Many ribosome profiling data processing tools have been developed. However, almost all tools analyze ribosome profiling data at the gene level. Since different isoforms of a gene may produce different proteins with distinct biological functions, it is advantageous to analyze ribosome profiling data at the isoform level. To meet this need, previously we developed a pipeline to analyze 610 public human ribosome profiling data at the isoform level and constructed HRPDviewer database.ResultsTo allow other researchers to use our pipeline as well, here we implement our pipeline as an easy-to-use software tool called RPiso. Compared to Ribomap (a widely used tool which provides isoform-level ribosome profiling analyses), our RPiso (1) estimates isoform abundance more accurately, (2) supports analyses on more species, and (3) provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms.ConclusionsIn this study, we developed RPiso software tool (http://cosbi7.ee.ncku.edu.tw/RPiso/) to provide isoform-level ribosome profiling analyses. RPiso is very easy to install and execute. RPiso also provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms. We believe that RPiso is a useful tool for researchers to analyze and visualize their own ribosome profiling data at the isoform level.

【 授权许可】

CC BY