School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47405, USA.
Nucleic Acids Res. 2019 Jul 2;47(W1):W289-W294. doi: 10.1093/nar/gkz329.
MyDGR is a web server providing integrated prediction and visualization of Diversity-Generating Retroelements (DGR) systems in query nucleotide sequences. It is built upon an enhanced version of DGRscan, a tool we previously developed for identification of DGR systems. DGR systems are remarkable genetic elements that use error-prone reverse transcriptases to generate vast sequence variants in specific target genes, which have been shown to benefit their hosts (bacteria, archaea or phages). As the first web server for annotation of DGR systems, myDGR is freely available on the web at http://omics.informatics.indiana.edu/myDGR with all major browsers supported. MyDGR accepts query nucleotide sequences in FASTA format, and outputs all the important features of a predicted DGR system, including a reverse transcriptase, a template repeat and one (or more) variable repeats and their alignment featuring A-to-N (N can be C, T or G) substitutions, and VR-containing target gene(s). In addition to providing the results as text files for download, myDGR generates a visual summary of the results for users to explore the predicted DGR systems. Users can also directly access pre-calculated, putative DGR systems identified in currently available reference bacterial genomes and a few other collections of sequences (including human microbiomes).
MyDGR 是一个网络服务器，提供查询核苷酸序列中多样性产生反转录元件（DGR）系统的综合预测和可视化。它建立在我们之前开发的用于识别 DGR 系统的工具 DGRscan 的增强版本之上。DGR 系统是一种非凡的遗传元件，它使用易错的逆转录酶在特定的靶基因中产生大量的序列变体，这些变体已被证明对其宿主（细菌、古菌或噬菌体）有益。作为第一个用于 DGR 系统注释的网络服务器，myDGR 可在 http://omics.informatics.indiana.edu/myDGR 上通过所有主流浏览器免费访问。myDGR 以 FASTA 格式接受查询核苷酸序列，并输出预测的 DGR 系统的所有重要特征，包括逆转录酶、模板重复和一个（或多个）可变重复及其特征为 A 到 N（N 可以是 C、T 或 G）取代的对齐，以及包含 VR 的靶基因。除了提供可下载的文本文件结果外，myDGR 还为用户生成了预测 DGR 系统的可视化摘要，供用户探索。用户还可以直接访问当前可用的参考细菌基因组和其他一些序列集合（包括人类微生物组）中预先计算的、假定的 DGR 系统。
