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DOE OSTI · 1827914

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
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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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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. 2020-10-27. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. https://doi.org/10.1093/nar%2Fgkaa921

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