Journal
BMC BIOINFORMATICS
Volume 22, Issue SUPPL 10, Pages -Publisher
BMC
DOI: 10.1186/s12859-021-04192-7
Keywords
Ribo-seq; Ribosome profiling; Pipeline; Tool; Software; Isoform-level; Visualization
Categories
Funding
- Ministry of Science and Technology of Taiwan [107-2221-E-006-225-MY3, 108-2628-E-006-004-MY3]
- NCI [RO1 CA204962]
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The study developed the RPiso software tool to provide isoform-level ribosome profiling analyses, which is easy to install and execute, and also provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms.
Background: Translational 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. Results: To 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. Conclusions: In 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.
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