ModrRNA1: A tool for rapid general identification of possible RNA modification sites in bacterial rRNA and prediction of the associated putative enzymes

Abstract

Ribosomal RNA modifications play a crucial role in bacteria, impacting function, ribosome formation, and antibiotic resistance. ModrRNA1 replaces manual methods and introduces a user-friendly, streamlined bioinformatics tool for the identification of potential rRNA modification sites and associated enzymes, across various bacteria. This tool utilizes a curated database of known bacterial rRNA modifications and enzymes, employing sequence alignment with a customized scoring system for precise site identification. High-confidence alignments generate annotated RNA sequence plots. Subsequently, enzyme detection is facilitated through structural comparisons, phylogenetics, and BLAST. ModrRNA1 boasts a user-friendly web interface hosted at https://modrrna.biotechie.org with the open-source code for customization available at https://github.com/sciguysl/ModrRNA1. The results demonstrate ModrRNA1s efficacy in identifying potential non-species-specific bacterial rRNA modification sites and species-specific associated enzymes.