🧬 Welcome to shinytRNA
An interactive web application to explore nuclear tRNA gene organization in plant organisms
About shinytRNA
shinytRNA is an interactive web application for analyzing and visualizing the organization of nuclear tRNA genes across photosynthetic organisms. shinytRNA enables users to move from raw genomic annotations to interpretable patterns of tRNA organization within minutes.
Developed as part of the analyses presented in our manuscript ([REF] or see below), it extends the PlantRNA 2.0 database by providing hands-on tools to explore whether tRNA genes are randomly distributed along chromosomes or follow specific organizational rules.
With shinytRNA, results can be directly visualized, exported as figures (PNG) or downloaded as table (CSV).
Typical Workflow
Follow these simple steps:
1. Select your species/genome build on the left panel '1. Data selection'
2. Choose a module from '2. Data analysis' (Isotype / Distance / Pairwise / Clusters / Centromere)
3. Adjust parameters (cluster rules, distance windows, etc.)
4. Inspect plots & tables
5. Export figures & data
🔬 Analysis Modules
tRNA Isotype
Quantify and map tRNA genes by amino-acid type per chromosome. Compare observed vs. expected counts, assuming tRNAs are randomly distributed according to chromosome length. Includes heatmaps and summary graphs to assess non-random enrichment or depletion.
Inter-tRNA Distance
Compute inter-tRNA distances (distance between consecutive tRNA genes) per chromosome. Summarize them as heatmaps and boxplots. Useful to detect spacing irregularities that deviate from random expectations.
tRNA Pairwise
Analyze patterns in consecutive tRNA pairs along chromosomes. Identify amino acid transitions that occur more or less frequently than expected by chance, revealing potential functional clustering or regulatory constraints.
tRNA Clusters
Identify tRNA gene clusters using customizable thresholds (minimum number of tRNAs per cluster and max/min allowed gaps). The tool reports cluster coordinates, composition (isotypes), and density, with tables and plots for easy interpretation.
Centromere Positioning
Estimate putative centromere positions from largest inter-tRNA gaps, displayed as chromosome schematics with tabulated coordinates. Accuracy depends on genome assembly quality and tRNA locus coverage.
How to Cite
The application is hosted and maintained by the Institut de biologie moléculaire des plantes (IBMP), CNRS / Université de Strasbourg, France, and accompanies the analyses described in our manuscript.
If shinytRNA supports your work, please cite:
XXX et al. (2024). [Publication title]. [Journal Name].
App URL:
https://[your-app-url]
PlantRNA 2.0:
http://plantrna.ibmp.cnrs.fr/