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

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

doi:10.1093/nar/gkaa921

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.

Highlights

RNAcentral is the non-coding RNA sequence database that currently integrates 44 specialist ncRNA databases, known as Expert Databases, to provide unified access to >18 million ncRNA sequences spanning a broad range of functions and species [1]
RNAcentral provides a wide range of annotation types, such as genome coordinates, microRNA–target interactions [2,3], Gene Ontology (GO) terms [4], orthologs and paralogs [5], RNA family classification from Rfam [6] and more
The primary goal of RNAcentral is to provide open access to a comprehensive set of ncRNA sequences for a wide range of species, enabling the users to find what is known about individual sequences or download ncRNA sequences and their genomic locations that can be used for a broad range of studies, such as interpreting the results of RNA-seq experiments or training bioinformatic algorithms

Summary

INTRODUCTION

RNAcentral is the non-coding RNA (ncRNA) sequence database that currently integrates 44 specialist ncRNA databases, known as Expert Databases, to provide unified access to >18 million ncRNA sequences spanning a broad range of functions and species [1]. RNAcentral provides a wide range of annotation types, such as genome coordinates, microRNA–target interactions [2,3], Gene Ontology (GO) terms [4], orthologs and paralogs [5], RNA family classification from Rfam [6] and more. The primary goal of RNAcentral is to provide open access to a comprehensive set of ncRNA sequences for a wide range of species, enabling the users to find what is known about individual sequences or download ncRNA sequences and their genomic locations that can be used for a broad range of studies, such as interpreting the results of RNA-seq experiments or training bioinformatic algorithms. The previous NAR publication is marked with a vertical dashed line

Transition to Sequence Ontology to annotate RNA types

CONCLUSIONS

Findings

24. Alliance of Genome Resources Consortium The alliance of genome Resources