DARNED: a DAtabase of RNa EDiting in humans

Motivation: 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. Results: 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.