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MyDGR: a server for identification and characterization of diversity-generating retroelements
1School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47405, USA.
Nucleic Acids Research
|May 4, 2019
Summary
MyDGR is a new web server for predicting and visualizing Diversity-Generating Retroelements (DGR) systems in DNA sequences. This tool aids in understanding these genetic elements and their role in host adaptation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Diversity-Generating Retroelements (DGR) are mobile genetic elements that generate genetic diversity in bacteria, archaea, and phages.
- These elements utilize error-prone reverse transcriptases to introduce sequence variations in target genes, potentially conferring adaptive advantages to their hosts.
- Understanding the distribution and function of DGR systems is crucial for deciphering microbial evolution and adaptation.
Purpose of the Study:
- To develop and present MyDGR, the first web server for the integrated prediction and visualization of DGR systems.
- To provide researchers with a user-friendly platform for identifying DGR components and analyzing their characteristics in nucleotide sequences.
- To facilitate the exploration of DGR systems in various genomic contexts, including reference bacterial genomes and microbiome datasets.
Main Methods:
- MyDGR is built upon an enhanced version of the DGRscan tool for DGR system identification.
- The web server accepts nucleotide sequences in FASTA format for analysis.
- It predicts key DGR features: reverse transcriptase, template repeat, variable repeats, and target genes, along with their alignments and substitutions.
Main Results:
- MyDGR successfully predicts and visualizes DGR systems, including their components and sequence variations.
- The server provides downloadable text files of predicted features and generates interactive visual summaries.
- Pre-calculated DGR systems from reference bacterial genomes and microbiome collections are accessible.
Conclusions:
- MyDGR serves as a valuable, freely accessible resource for the identification and analysis of DGR systems.
- The tool enhances the study of genetic variation and host-microbe interactions mediated by DGR elements.
- MyDGR is expected to advance research into the evolutionary roles of DGR systems across diverse microbial communities.
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