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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

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.

In: Nucleic Acids Research, Vol. 49, No. D1, 2021, p. D212-D220.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Sweeney, BA, Petrov, AI, Ribas, CE, Finn, RD, Bateman, A, Szymanski, M, Karlowski, WM, Seemann, SE, Gorodkin, J, Cannone, JJ, Gutell, RR, Kay, S, Marygold, S, Dos Santos, G, Frankish, A, Mudge, JM, Barshir, R, Fishilevich, S, Chan, PP, Lowe, TM, Seal, R, Bruford, E, Panni, S, Porras, P, Karagkouni, D, Hatzigeorgiou, AG, Ma, L, Zhang, Z, Volders, PJ, Mestdagh, P, Griffiths-Jones, S, Fromm, B, Peterson, KJ, Kalvari, I, Nawrocki, EP, Petrov, AS, Weng, S, Bouchard-Bourelle, P, Scott, M, Lui, LM, Hoksza, D, Lovering, RC, Kramarz, B, Mani, P, Ramachandran, S & Weinberg, Z 2021, 'RNAcentral 2021: Secondary structure integration, improved sequence search and new member databases', Nucleic Acids Research, vol. 49, no. D1, pp. D212-D220. https://doi.org/10.1093/nar/gkaa921

APA

Sweeney, B. A., Petrov, A. I., Ribas, C. E., Finn, R. D., Bateman, A., Szymanski, M., Karlowski, W. M., Seemann, S. E., Gorodkin, J., Cannone, J. J., Gutell, R. R., Kay, S., Marygold, S., Dos Santos, G., Frankish, A., Mudge, J. M., Barshir, R., Fishilevich, S., Chan, P. P., ... Weinberg, Z. (2021). RNAcentral 2021: Secondary structure integration, improved sequence search and new member databases. Nucleic Acids Research, 49(D1), D212-D220. https://doi.org/10.1093/nar/gkaa921

Vancouver

Sweeney BA, Petrov AI, Ribas CE, Finn RD, Bateman A, Szymanski M et al. RNAcentral 2021: Secondary structure integration, improved sequence search and new member databases. Nucleic Acids Research. 2021;49(D1):D212-D220. https://doi.org/10.1093/nar/gkaa921

Author

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. / RNAcentral 2021 : Secondary structure integration, improved sequence search and new member databases. In: Nucleic Acids Research. 2021 ; Vol. 49, No. D1. pp. D212-D220.

Bibtex

@article{1ca584341c1b4c0480cc0b7bdae94043,
title = "RNAcentral 2021: Secondary structure integration, improved sequence search and new member databases",
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. ",
author = "Sweeney, {Blake A.} and Petrov, {Anton I.} and Ribas, {Carlos E.} and Finn, {Robert D.} and Alex Bateman and MacIej Szymanski and Karlowski, {Wojciech M.} and Seemann, {Stefan E.} and Jan Gorodkin and Cannone, {Jamie J.} and Gutell, {Robin R.} and Simon Kay and Steven Marygold and {Dos Santos}, Gil and Adam Frankish and Mudge, {Jonathan M.} and Ruth Barshir and Simon Fishilevich and Chan, {Patricia P.} and Lowe, {Todd M.} and Ruth Seal and Elspeth Bruford and Simona Panni and Pablo Porras and Dimitra Karagkouni and Hatzigeorgiou, {Artemis G.} and Lina Ma and Zhang Zhang and Volders, {Pieter Jan} and Pieter Mestdagh and Sam Griffiths-Jones and Bastian Fromm and Peterson, {Kevin J.} and Ioanna Kalvari and Nawrocki, {Eric P.} and Petrov, {Anton S.} and Shuai Weng and Philia Bouchard-Bourelle and Michelle Scott and Lui, {Lauren M.} and David Hoksza and Lovering, {Ruth C.} and Barbara Kramarz and Prita Mani and Sridhar Ramachandran and Zasha Weinberg",
year = "2021",
doi = "10.1093/nar/gkaa921",
language = "English",
volume = "49",
pages = "D212--D220",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "D1",

}

RIS

TY - JOUR

T1 - RNAcentral 2021

T2 - Secondary structure integration, improved sequence search and new member databases

AU - Sweeney, Blake A.

AU - Petrov, Anton I.

AU - Ribas, Carlos E.

AU - Finn, Robert D.

AU - Bateman, Alex

AU - Szymanski, MacIej

AU - Karlowski, Wojciech M.

AU - Seemann, Stefan E.

AU - Gorodkin, Jan

AU - Cannone, Jamie J.

AU - Gutell, Robin R.

AU - Kay, Simon

AU - Marygold, Steven

AU - Dos Santos, Gil

AU - Frankish, Adam

AU - Mudge, Jonathan M.

AU - Barshir, Ruth

AU - Fishilevich, Simon

AU - Chan, Patricia P.

AU - Lowe, Todd M.

AU - Seal, Ruth

AU - Bruford, Elspeth

AU - Panni, Simona

AU - Porras, Pablo

AU - Karagkouni, Dimitra

AU - Hatzigeorgiou, Artemis G.

AU - Ma, Lina

AU - Zhang, Zhang

AU - Volders, Pieter Jan

AU - Mestdagh, Pieter

AU - Griffiths-Jones, Sam

AU - Fromm, Bastian

AU - Peterson, Kevin J.

AU - Kalvari, Ioanna

AU - Nawrocki, Eric P.

AU - Petrov, Anton S.

AU - Weng, Shuai

AU - Bouchard-Bourelle, Philia

AU - Scott, Michelle

AU - Lui, Lauren M.

AU - Hoksza, David

AU - Lovering, Ruth C.

AU - Kramarz, Barbara

AU - Mani, Prita

AU - Ramachandran, Sridhar

AU - Weinberg, Zasha

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkaa921

DO - 10.1093/nar/gkaa921

M3 - Journal article

C2 - 33106848

AN - SCOPUS:85099429146

VL - 49

SP - D212-D220

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -

ID: 259671031