Biochemistry Department, University College Cork, Ireland.
Bioinformatics. 2010 Jul 15;26(14):1772-6. doi: 10.1093/bioinformatics/btq285. Epub 2010 Jun 14.
RNA editing is a phenomenon, which is responsible for the alteration of particular nucleotides in RNA sequences relative to their genomic templates. Recently, a large number of RNA editing instances in humans have been identified using bioinformatic screens and high-throughput experimental investigations utilizing next-generation sequencing technologies. However, the available data on RNA editing are not uniform and difficult to access.
Here, we describe a new database DARNED (DAtabase of RNa EDiting) that provides centralized access to available published data related to RNA editing. RNA editing locations are mapped on the reference human genome. The current release of the database contains information on approximately 42 000 human genome coordinates corresponding to RNA locations that undergo RNA editing, mostly involving adenosine-to-inosine (A-to-I) substitutions. The data can be queried using a range of genomic coordinates, their corresponding functional localization in RNA molecules [Exons, Introns, CoDing Sequence (CDS) and UnTranslated Regions (UTRs)] and information regarding tissue/organ/cell sources where RNA editing has been observed. It is also possible to obtain RNA editing information for a specific gene or an RNA molecule using corresponding accession numbers. Search results provide information on the number of expressed sequence tags (ESTs) supporting edited and genomic bases, functional localization of RNA editing and existence of known single nucleotide polymorphisms (SNPs). Editing data can be explored in UCSC and Ensembl genome browsers, in conjunction with additional data provided by these popular genome browsers. DARNED has been designed for researchers seeking information on RNA editing and for the developers of novel algorithms for its prediction.
DARNED is accessible at http://darned.ucc.ie
RNA 编辑是一种现象，它负责相对于其基因组模板改变 RNA 序列中特定核苷酸。最近，利用生物信息学筛选和利用下一代测序技术的高通量实验研究，已经在人类中鉴定出大量的 RNA 编辑实例。然而，可用的 RNA 编辑数据并不统一，也难以访问。
在这里，我们描述了一个新的数据库 DARNED（RNA 编辑数据库），它提供了对与 RNA 编辑相关的可用已发表数据的集中访问。RNA 编辑位置被映射到参考人类基因组上。该数据库的当前版本包含约 42000 个人类基因组坐标的信息，这些坐标对应于经历 RNA 编辑的 RNA 位置，主要涉及腺苷到肌苷（A-to-I）取代。可以使用一系列基因组坐标、它们在 RNA 分子中的相应功能定位（外显子、内含子、编码序列（CDS）和非翻译区（UTRs））以及观察到 RNA 编辑的组织/器官/细胞来源信息来查询数据。还可以使用相应的访问号获取特定基因或 RNA 分子的 RNA 编辑信息。搜索结果提供了支持编辑和基因组碱基的表达序列标签（EST）数量、RNA 编辑的功能定位以及已知单核苷酸多态性（SNP）的信息。可以与这些流行的基因组浏览器提供的其他数据一起，在 UCSC 和 Ensembl 基因组浏览器中探索编辑数据。DARNED 是为寻求 RNA 编辑信息的研究人员以及为其预测开发新算法的人员设计的。
DARNED 可在 http://darned.ucc.ie 访问
