Rfam: Towards a sustainable resource for understanding the genomic functional ncRNA repertoire

Rfam：寻找了解基因组功能 ncRNA 库的可持续资源

• 批准号: BB/M011690/1
• 负责人: Alex Bateman
• 金额: $ 54.53万
• 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: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM011690%2F1
• 关键词: Rfam; Towards; sustainable; resource; understanding

In molecular biology, the central dogma says that genes encoded in a genome code for RNA, which is then translated into the proteins carrying out the main processes of the cell. But, RNA is not just an intermediate step between genes and protein. Instead, RNA is capable of performing a number of tasks that are essential for life - for example, the ribosome (the machine responsible for synthesizing proteins from RNA) is an RNA-based machine, and RNA plays important roles in regulating the levels of other genes. These RNAs involved in biology are known as non-coding RNAs (ncRNA).RNA research has lagged behind that of proteins, in part due to the difficulties in working with them experimentally and computationally. The field of RNA biology is comparatively poorly served with resources that can aid research when compared with protein science. Rfam is one of the largest and most authoritative sources on ncRNA information, and provides a central portal of information covering a wide variety of ncRNA types. We use statistical models to group related non-coding RNAs into families. We then provide information on their function, as well as providing tools which other scientists can use to discover related non-coding RNAs in their samples of interest. A primary use of our database is to identify ncRNAs in DNA sequences. This allows scientists to map the positions of ncRNAs and study how ncRNAs have evolved between related organisms giving clues to their function. We aim to facilitate this further by providing families of ncRNAs from organisms which have had their entire genome sequenced. These organisms are generally those which are of interest to scientists because of their role in disease (e.g. pathogenic bacteria), their economic importance (e.g bread wheat, a major source of human nutrition), or because they occupy an important biological niche (e.g, humans). We'll also provide researchers with tools and training to build their own RNA families, allowing them to study RNAs which are of particular interest to them. Not only is it important to be able to identify a ncRNA, it's also important for us to tell our users what the function of an ncRNA is. To this end, we are improving our functional annotation of our RNA families, by using structured language terms that are easily parseable by both humans and computers. This means that our large data sets can be mined quickly, allowing researchers to build up a picture of how ncRNAs interact with the rest of the cell's components and understand more about the roles ncRNA play in biological systems.All our information is freely available via the Rfam website and as a downloadable database. We also export our data to other resources, such as databases concerned with a specific organism, and more general RNA databases such as RNAcentral.

在分子生物学中，中心法则说，基因组中编码的基因编码RNA，然后翻译成蛋白质，执行细胞的主要过程。但是，RNA不仅仅是基因和蛋白质之间的中间步骤。相反，RNA能够执行许多对生命至关重要的任务-例如，核糖体（负责从RNA合成蛋白质的机器）是一个基于RNA的机器，RNA在调节其他基因的水平方面发挥着重要作用。这些参与生物学的RNA被称为非编码RNA（ncRNA）。RNA的研究落后于蛋白质，部分原因是在实验和计算上与它们合作的困难。与蛋白质科学相比，RNA生物学领域的资源相对较少，可以帮助研究。Rfam是最大和最权威的ncRNA信息来源之一，提供了一个涵盖各种ncRNA类型的信息中心门户。我们使用统计模型将相关的非编码RNA分组到家族中。然后，我们提供有关其功能的信息，并提供其他科学家可以用来在他们感兴趣的样品中发现相关非编码RNA的工具。我们的数据库的主要用途是识别DNA序列中的ncRNA。这使科学家能够绘制ncRNA的位置，并研究ncRNA如何在相关生物体之间进化，从而为它们的功能提供线索。我们的目标是通过提供来自生物体的ncRNA家族来进一步促进这一点，这些生物体已经对其整个基因组进行了测序。这些生物通常是科学家感兴趣的生物，因为它们在疾病中的作用（例如致病菌），它们的经济重要性（例如面包小麦，人类营养的主要来源），或者因为它们占据了重要的生物生态位（例如人类）。我们还将为研究人员提供工具和培训，以建立他们自己的RNA家族，使他们能够研究他们特别感兴趣的RNA。不仅能够识别ncRNA很重要，告诉我们的用户ncRNA的功能也很重要。为此，我们正在改进我们的RNA家族的功能注释，通过使用易于由人类和计算机解析的结构化语言术语。这意味着我们的大数据集可以被快速挖掘，使研究人员能够建立ncRNA如何与细胞的其他成分相互作用的图片，并了解更多关于ncRNA在生物系统中发挥的作用。我们所有的信息都可以通过Rfam网站免费获得，也可以作为下载数据库。我们还将我们的数据导出到其他资源，例如与特定生物有关的数据库，以及更通用的RNA数据库，如RNAcentral。

项目成果

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

• DOI: 10.1093/nar/gkaa1047
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kalvari I;Nawrocki EP;Ontiveros-Palacios N;Argasinska J;Lamkiewicz K;Marz M;Griffiths-Jones S;Toffano-Nioche C;Gautheret D;Weinberg Z;Rivas E;Eddy SR;Finn RD;Bateman A;Petrov AI
• 通讯作者: Petrov AI

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.

• DOI: 10.1093/nar/gkx1038
• 发表时间: 2018-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kalvari I;Argasinska J;Quinones-Olvera N;Nawrocki EP;Rivas E;Eddy SR;Bateman A;Finn RD;Petrov AI
• 通讯作者: Petrov AI

Non-Coding RNA Analysis Using the Rfam Database.

• DOI: 10.1002/cpbi.51
• 发表时间: 2018-06
• 期刊: Current protocols in bioinformatics
• 作者: Kalvari I;Nawrocki EP;Argasinska J;Quinones-Olvera N;Finn RD;Bateman A;Petrov AI
• 通讯作者: Petrov AI