myDGR

myDGR detects and predicts diversity-generating retroelements (DGRs) in nucleotide sequences to characterize reverse transcriptases, template repeats, variable repeats with A-to-N (where N can be C, T, or G) substitutions, and VR-containing target genes in bacteria, archaea, and phages.

Key Features:

• Identification and Prediction: Leverages characteristics of error-prone reverse transcriptases to identify genetic elements that generate extensive sequence variation in specific target genes across bacteria, archaea, and phages.
• Input and Output Formats: Accepts nucleotide sequences in FASTA format and outputs predicted DGR components including reverse transcriptase genes, template repeats, variable repeats with A-to-N (where N can be C, T, or G) substitutions, and VR-containing target genes.
• Pre-calculated Datasets: Includes pre-calculated putative DGR systems identified in reference bacterial genomes and sequence collections such as human microbiomes.
• Algorithmic Basis: Implements an enhanced version of DGRscan with advanced algorithms for the accurate prediction of DGR systems.

Scientific Applications:

• DGR discovery in microbial genomes: Enables identification of putative DGRs and their components in bacterial, archaeal, and phage nucleotide sequences.
• Mechanistic studies of genetic diversification: Supports analysis of A-to-N substitution patterns and reverse transcriptase-associated diversification mechanisms.
• Evolutionary and comparative genomics: Facilitates investigations into how DGRs contribute to host adaptability and evolutionary processes in microorganisms.
• Microbiome sequence analysis: Allows exploration of putative DGR systems within human microbiome and other sequence collections.

Methodology:

Built upon an enhanced version of DGRscan, the method analyzes nucleotide sequences to identify reverse transcriptases, template repeats, and variable repeats exhibiting A-to-N substitutions.