RSVdb: a comprehensive database of transcriptome RNA structure. Issue 3 (8th May 2020)

• Record Type: Journal Article
• Authors: Yu, Haopeng; Zhang, Yi; Sun, Qing; Gao, Huijie; Tao, Shiheng
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 3(2021)
• Publication Date: 2020-05-08
• Subjects: RSVdb -- transcriptome RNA structure database -- dimethyl sulfate probing -- RT-stop method -- MaP method -- RNA structure prediction; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbaa071
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: 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 probe the RNA structure at the transcriptome level effectively. 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 eight 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.