RNAcentral: a hub of information for non-coding RNA sequences

Journal Article · Sat Dec 08 00:00:00 EST 2018 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gky1206· OSTI ID:1629057

Sweeney, Blake A. ; Petrov, Anton I. ; Burkov, Boris; Finn, Robert D. ; Bateman, Alex ; Szymanski, Maciej; Karlowski, Wojciech M.; Gorodkin, Jan; Seemann, Stefan E.; Cannone, Jamie J.; Gutell, Robin R.; Fey, Petra; Basu, Siddhartha; Kay, Simon; Cochrane, Guy ; Billis, Kostantinos; Emmert, David; Marygold, Steven J.; Huntley, Rachael P. ; Lovering, Ruth C. ; Frankish, Adam; Chan, Patricia P.; Lowe, Todd M. ; Bruford, Elspeth ; Seal, Ruth; Vandesompele, Jo ; Volders, Pieter-Jan ; Paraskevopoulou, Maria; Ma, Lina; Zhang, Zhang; Griffiths-Jones, Sam; Bujnicki, Janusz M.; Boccaletto, Pietro; Blake, Judith A. ; Bult, Carol J.; Chen, Runsheng; Zhao, Yi; Wood, Valerie; Rutherford, Kim; Rivas, Elena ; Cole, James; Laulederkind, Stanley J. F. ; Shimoyama, Mary; Gillespie, Marc E.; Orlic-Milacic, Marija; Kalvari, Ioanna ; Nawrocki, Eric ; Engel, Stacia R.; Cherry, J. Michael ; Team, SILVA; Berardini, Tanya Z.; Hatzigeorgiou, Artemis; Karagkouni, Dimitra; Howe, Kevin ; Davis, Paul; Dinger, Marcel; He, Shunmin ; Yoshihama, Maki; Kenmochi, Naoya; Stadler, Peter F.; Williams, Kelly P.

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality.

• Sponsoring Organization: USDOE
• Contributing Organization: The RNAcentral Consortium
• DOE Contract Number: NA0003525
• OSTI ID: 1629057
• Journal Information: Nucleic Acids Research, Vol. 47, Issue D1; ISSN 0305-1048
• Publisher: Oxford University Press
• Country of Publication: United States
• Language: English