myRT

myRT identifies and classifies Reverse Transcriptases (RTs) in bacterial genomes and metagenomes to characterize RT classes and their genomic neighborhoods.

Key Features:

• RT detection: Identifies Reverse Transcriptases (RTs) within bacterial genomes and metagenomes.
• RT classification: Classifies RTs into prokaryotic RT classes including group II introns, Diversity Generating Retroelements (DGRs), retrons, CRISPR-Cas–associated RTs, and Abortive Infection (Abi)–associated RTs.
• Genomic neighborhood analysis: Analyzes genomic neighborhood of RTs to provide functional clues about RT roles and mechanisms.
• Large-scale genome screening: Applied to all complete and draft bacterial genomes to generate a curated collection of putative RTs.
• Metagenome profiling: Applied to gut metagenomes to compare RT class abundances, reporting a higher proportion of DGR-related RTs than retron-related RTs in gut samples.

Scientific Applications:

• RT repertoire characterization: Characterize the distribution and diversity of Reverse Transcriptases (RTs) across bacterial genomes and metagenomes.
• Functional inference of RT-associated systems: Infer functions of RTs in group II introns, DGRs, retrons, CRISPR-Cas systems, and Abi systems using classification and neighborhood context.
• Comparative metagenomics: Compare prevalence of RT classes between reference genomes and complex microbial communities such as gut microbiomes.
• Microbial genetics and evolution: Provide annotated RT datasets to support studies of microbial genetics and evolutionary dynamics.

Methodology:

Applied to all complete and draft bacterial genomes to produce a curated collection of putative RTs and applied to gut metagenomes to assess RT class abundance.