RNaseViz is a web-based application built with R Shiny, providing an interactive platform for visualizing RNase sequences, their conservation across different species, and the mutations associated with Mendelian diseases. https://norreanea.shinyapps.io/RNaseViz/
This tool was developed as part of the article Ribonucleases in Mendelian disease: Characterization and insight from model organisms
- Selection of RNase enzymes from a curated list of disease-relevant ribonucleases.
- Visualization of sequence conservation across orthologs using multiple sequence alignments.
- Overview cards summarizing the selected RNase, curated variants, available orthologs, scientific context, and organism abbreviations.
- Display of ortholog trees and domain organization figures for supported RNases.
- Residue-level inspection by clicking the alignment or entering a reference-sequence position manually.
- Download of whole alignments as FASTA files or annotated PDF figures with marked pathogenic variants.
- Support for multiple RNase enzymes associated with Mendelian disease.
To use the RNaseViz application:
- RNase selector: Choose the RNase family member to analyze
- Reference organism selector: Select the species whose sequence will be used as the positional reference for residue mapping.
- Residue / Variant query box: Enter a residue number or mutation label to jump directly to a selected site in the alignment.
- Alignment download panel: Choose the export format and download either the FASTA alignment or an annotated PDF with marked pathogenic variants.
- Pathway overview figure: A figure linking the selected RNase to its biological pathway and disease context.
- Main navigation tabs: Switch between the two views: Overview and Alignment.
- Summary cards**: The number of curated variants/regions and available orthologs.
- Scientific context panel: Brief biological summary of the selected RNase, including function, disease relevance, and highlighted pathogenic variants.
- Ortholog phylogenetic tree: Shows evolutionary relationships among orthologs of the selected RNase across species.
- Organism abbreviations
- Curated variant table: Interactive table listing pathogenic or otherwise marked residues/regions, searchable and filterable by organism and aligned position.
- Residue inspection summary: Displays the currently selected residue, its aligned coordinate, conservation level, and nearby curated features.
- Domain organization panel: Shows protein architecture across species, with domains and marked disease-associated residues positioned along the sequence.
- Domain figure legend: Explains how to read the domain map, including aligned positions, exon deletions, domain colors, and mutation markers.
- Multiple sequence alignment viewer: Comparative visualization showing residue conservation, mismatches, gaps, and the positions of curated variants across orthologs.
Below is the example of DICER1 alignment report from RNaseViz. The human sequence is aligned with orthologs from other species, and disease-associated mutations are marked directly on the alignment. The colors correspond to different diseases, and each mutation label is linked to corresponding ClinVar page.
For questions or support, please open an issue on this GitHub repository.