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

Sweeney, Blake A.; Petrov, Anton I.; Ribas, Carlos E.; Finn, Robert D.; Bateman, Alex; Szymanski, Maciej; Karlowski, Wojciech M.; Seemann, Stefan E.; Gorodkin, Jan; Cannone, Jamie J.; Gutell, Robin R.; Kay, Simon; Marygold, Steven; dos Santos, Gil; Frankish, Adam; Mudge, Jonathan M.; Barshir, Ruth; Fishilevich, Simon; Chan, Patricia P.; Lowe, Todd M.; Seal, Ruth; Bruford, Elspeth; Panni, Simona; Porras, Pablo; Karagkouni, Dimitra; Hatzigeorgiou, Artemis G.; Ma, Lina; Zhang, Zhang; Volders, Pieter-Jan; Mestdagh, Pieter; Griffiths-Jones, Sam; Fromm, Bastian; Peterson, Kevin J.; Kalvari, Ioanna; Nawrocki, Eric P.; Petrov, Anton S.; Weng, Shuai; Bouchard-Bourelle, Philia; Scott, Michelle; Lui, Lauren M.; Hoksza, David; Lovering, Ruth C.; Kramarz, Barbara; Mani, Prita; Ramachandran, Sridhar; Weinberg, Zasha

doi:10.1093/nar/gkaa921

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

Journal Article · Tue Oct 27 00:00:00 EDT 2020 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkaa921· OSTI ID:1827914

Sweeney, Blake A.; Petrov, Anton I.; Ribas, Carlos E.; Finn, Robert D.; Bateman, Alex; Szymanski, Maciej; Karlowski, Wojciech M.; Seemann, Stefan E.; Gorodkin, Jan; Cannone, Jamie J.; Gutell, Robin R.; Kay, Simon; Marygold, Steven; dos Santos, Gil; Frankish, Adam; Mudge, Jonathan M.; Barshir, Ruth; Fishilevich, Simon; Chan, Patricia P.; Lowe, Todd M. more »

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: Biotechnology and Biological Sciences Research Council (BBSRC); National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER); Wellcome Trust

Contributing Organization:: RNAcentral Consortium

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1827914

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 49; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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