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

Abstract

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.

A review of Ribosome profiling and tools used in Ribo-seq data analysis

“… Eukaryotes RiboToolkit [30] 2020 Perl, R, Java Fastq/FASTA file Adapter trimming Read mapping Codon usage analysis Metagene analysis Translation efficiency calculation Differential translation analysis Functional annotation analysis The first integrated one-stop web server for Ribo-seq data analysis Prokaryotes and eukaryotes RiboVIEW [43] 2020 R, Python BAM file Periodicity calculation Metagene analysis Condon enrichment analysis Condon occupancy analysis Visualization of translation elongation at the codon level. Unbiased estimates of codon enrichment Prokaryotes and eukaryotes RPiso [44] 2021 Perl, Python Fastq file Adapter trimming Read mapping mRNA isoform visualization More reliable and precise results of isoform abundance. Eukaryotes RP-REP [45] 2021 Perl, R, Python Gene Matrix Transposed (GMT) files, XLSX file Adapter trimming Read mapping Principal component analysis Differential expression analysis Functional enrichment analysis Vertical scaling of processing up to96 cores The Snakemake workflow management system Prokaryotes and eukaryotes Ribotracer [23] 2019 Jupyter Notebook, Python BAM file, FASTA file, GTF file …”