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RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral Consortium. Nucleic Acids Res. .

Abstract

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.

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Figures

Figure 1.
Figure 1.
Growth in the number of RNAcentral Expert Databases since its launch in 2014 (for an up-to-date list see https://rnacentral.org/expert-databases). The previous NAR publication is marked with a vertical dashed line.
Figure 2.
Figure 2.
(A) The RNAcentral text search results include simplified thumbnails representing the 2D structures. (B) A 2D structure of the human LSU rRNA displayed on the sequence report page for URS000075EC78_9606.
Figure 3.
Figure 3.
New RNAcentral sequence similarity search interface. (A) Query sequence, (B) Identical sequence found in RNAcentral, (C) Secondary structure visualized with R2DT, (D) Rfam classification, including Rfam family annotations and an alignment between the query and the Rfam model, (E) Similar sequences found in RNAcentral that can be filtered using facets, such as RNA types and Organisms, sorted or downloaded.
Figure 4.
Figure 4.
The distribution of RNAcentral sequences by the SO terms.
See this image and copyright information in PMC

References

    1. RNAcentral Consortium RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res. 2019; 47:D221–D229. - PMC - PubMed
    1. Karagkouni D., Paraskevopoulou M.D., Chatzopoulos S., Vlachos I.S., Tastsoglou S., Kanellos I., Papadimitriou D., Kavakiotis I., Maniou S., Skoufos G. et al. .. DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions. Nucleic Acids Res. 2018; 46:D239–D245. - PMC - PubMed
    1. Paraskevopoulou M.D., Vlachos I.S., Karagkouni D., Georgakilas G., Kanellos I., Vergoulis T., Zagganas K., Tsanakas P., Floros E., Dalamagas T. et al. .. DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res. 2016; 44:D231–D238. - PMC - PubMed
    1. Binns D., Dimmer E., Huntley R., Barrell D., O’Donovan C., Apweiler R.. QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics. 2009; 25:3045–3046. - PMC - PubMed
    1. Pignatelli M., Vilella A.J., Muffato M., Gordon L., White S., Flicek P., Herrero J.. ncRNA orthologies in the vertebrate lineage. Database:J. Biol. Database. Curat. 2016; 2016:bav127. - PMC - PubMed

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