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RSVdb: A comprehensive database of transcriptome RNA structure

By Haopeng Yu, Yi Zhang, Qing Sun, Huijie Gao, Shiheng Tao

Posted 21 Jul 2019
bioRxiv DOI: 10.1101/710236 (published DOI: 10.1093/bib/bbaa071)

RNA fulfills a crucial regulatory role in cells by folding into a complex RNA structure. To date, a chemical compound, dimethyl sulfate (DMS), has been developed to effectively probe the RNA structure at the transcriptome level. We proposed a database, RSVdb (<https://taolab.nwafu.edu.cn/rsvdb/>), for the browsing and visualization of transcriptome RNA structures. RSVdb, including 626,225 RNAs with validated DMS reactivity from 178 samples in 8 species, supports four main functions: information retrieval, research overview, structure prediction, and resource download. Users can search for species, studies, transcripts and genes of interest; browse the quality control of sequencing data and statistical charts of RNA structure information; preview and perform online prediction of RNA structures in silico and under DMS restraint of different experimental treatments; and download RNA structure data for species and studies. Together, RSVdb provides a reference for RNA structure and will support future research on the function of RNA structure at the transcriptome level.

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