The RNAcentral database of non-coding RNAs

非编码RNA的RNA中央数据库

• 批准号: BB/J019232/1
• 负责人: Alex Bateman
• 金额: $ 12.67万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FJ019232%2F1
• 关键词: RNAcentral; database; non; coding; RNAs

In molecular biology, the central dogma says that the genes in DNA code for RNA. RNA molecules are then translated into proteins that are the mini-machines that carry out the main processes in the cell. It is only recently apparent that many genes code for RNAs, which are not translated into proteins, and which carry out important functions in the cell as RNA. These molecules are often known as non-coding RNAs. Much of the focus in biology has been on DNA and proteins, but recently there has been a surge of interest in non-coding RNAs. In fact, the mini-machine that makes proteins from RNA, called the ribosome, has itself been shown to be an RNA-based machine. Non-coding RNAs have also been shown to be widely involved in regulating the levels of other genes.Research and innovation in the area of non-coding RNAs, and in molecular biology more generally, is hampered by the lack of an authorative and comprehensive resource collecting together all known non-coding RNAs. There are over 20 different online databases that contain information about different types of RNA molecules. Each of these resources makes their information available in different ways. The scattered nature of these resources makes it nearly impossible for biologists to discover what is known about non-coding RNAs related to their research area. In this proposal, we will create a new online resource to collect together information about non-coding RNAs. This resource, called RNAcentral, will be a central warehouse for holding many types of information. The most important information stored is called the sequence of the RNA. Many existing RNA resources (called RNAcentral Expert Databases) will provide their data to RNAcentral using software and interfaces that will be created as part of this proposal. One specific expert database, called miRBase, based at the University of Manchester, will test out the systems for providing data to RNAcentral. RNAcentral will hold the common information about each type of RNA. For more specialised information, RNAcentral will provide links back to the RNAcentral Expert Databases.In order to make the RNAcentral resource cost effective, we will be reusing and modifying code that is already in use by the European Nucleotide Archive and Ensembl Genomes. These two databases are based at the European Bioinformatics Institute near Cambridge. By the end of this project, researchers from around the UK and the rest of the world will have access to a single resource of RNA sequence information. This information will be freely available in a variety of ways including via a website and as a downloadable database.

在分子生物学中，中心法则说 DNA 中的基因编码 RNA。然后 RNA 分子被翻译成蛋白质，蛋白质是执行细胞内主要过程的微型机器。直到最近才发现，许多基因编码 RNA，这些 RNA 不翻译成蛋白质，而是像 RNA 一样在细胞中发挥重要功能。这些分子通常被称为非编码 RNA。生物学界的大部分焦点都集中在 DNA 和蛋白质上，但最近人们对非编码 RNA 的兴趣激增。事实上，从 RNA 制造蛋白质的微型机器（称为核糖体）本身已被证明是一种基于 RNA 的机器。非编码 RNA 还被证明广泛参与调节其他基因的水平。非编码 RNA 领域以及更广泛的分子生物学领域的研究和创新因缺乏权威和全面的资源而受到阻碍将所有已知的非编码 RNA 收集在一起。有 20 多个不同的在线数据库包含有关不同类型 RNA 分子的信息。这些资源中的每一个都以不同的方式提供信息。这些资源的分散性使得生物学家几乎不可能发现与其研究领域相关的非编码 RNA 的已知信息。在本提案中，我们将创建一个新的在线资源来收集有关非编码 RNA 的信息。该资源称为 RNAcentral，将成为保存多种类型信息的中央仓库。存储的最重要的信息称为 RNA 序列。许多现有的 RNA 资源（称为 RNAcentral 专家数据库）将使用作为本提案一部分创建的软件和界面向 RNAcentral 提供数据。曼彻斯特大学的一个名为 miRBase 的特定专家数据库将测试向 RNAcentral 提供数据的系统。 RNAcentral 将保存每种类型 RNA 的共同信息。如需更多专业信息，RNAcentral 将提供返回 RNAcentral 专家数据库的链接。为了使 RNAcentral 资源具有成本效益，我们将重用和修改欧洲核苷酸档案库和 Ensembl Genomes 已使用的代码。这两个数据库位于剑桥附近的欧洲生物信息学研究所。到该项目结束时，英国各地和世界其他地区的研究人员将能够访问 RNA 序列信息的单一资源。该信息将通过多种方式免费提供，包括通过网站和可下载的数据库。

项目成果

RNAcentral: a comprehensive database of non-coding RNA sequences.

• DOI: 10.1093/nar/gkw1008
• 发表时间: 2017-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: The RNAcentral Consortium;Petrov AI;Kay SJE;Kalvari I;Howe KL;Gray KA;Bruford EA;Kersey PJ;Cochrane G;Finn RD;Bateman A;Kozomara A;Griffiths-Jones S;Frankish A;Zwieb CW;Lau BY;Williams KP;Chan PP;Lowe TM;Cannone JJ;Gutell R;Machnicka MA;Bujnicki JM;Yoshihama M;Kenmochi N;Chai B;Cole JR;Szymanski M;Karlowski WM;Wood V;Huala E;Berardini TZ;Zhao Y;Chen R;Zhu W;Paraskevopoulou MD;Vlachos IS;Hatzigeorgiou AG;Ma L;Zhang Z;Puetz J;Stadler PF;McDonald D;Basu S;Fey P;Engel SR;Cherry JM;Volders PJ;Mestdagh P;Wower J;Clark MB;Quek XC;Dinger ME
• 通讯作者: Dinger ME

The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI.

• DOI: 10.1093/nar/gkv316
• 发表时间: 2015-07-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Squizzato S;Park YM;Buso N;Gur T;Cowley A;Li W;Uludag M;Pundir S;Cham JA;McWilliam H;Lopez R
• 通讯作者: Lopez R

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

• DOI: 10.1093/nar/gkaa921
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: RNAcentral Consortium

RNAcentral: an international database of ncRNA sequences.

• DOI: 10.1093/nar/gku991
• 发表时间: 2015-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: RNAcentral Consortium;Petrov AI;Kay SJE;Gibson R;Kulesha E;Staines D;Bruford EA;Wright MW;Burge S;Finn RD;Kersey PJ;Cochrane G;Bateman A;Griffiths-Jones S;Harrow J;Chan PP;Lowe TM;Zwieb CW;Wower J;Williams KP;Hudson CM;Gutell R;Clark MB;Dinger M;Quek XC;Bujnicki JM;Chua NH;Liu J;Wang H;Skogerbø G;Zhao Y;Chen R;Zhu W;Cole JR;Chai B;Huang HD;Huang HY;Cherry JM;Hatzigeorgiou A;Pruitt KD
• 通讯作者: Pruitt KD

R2DT is a framework for predicting and visualising RNA secondary structure using templates.

• DOI: 10.1038/s41467-021-23555-5
• 发表时间: 2021-06-09
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Sweeney BA;Hoksza D;Nawrocki EP;Ribas CE;Madeira F;Cannone JJ;Gutell R;Maddala A;Meade CD;Williams LD;Petrov AS;Chan PP;Lowe TM;Finn RD;Petrov AI
• 通讯作者: Petrov AI