Department of Bioengineering, Faculty of Engineering, Imperial College London, London, United Kingdom.
Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.
PLoS One. 2021 Jan 15;16(1):e0245280. doi: 10.1371/journal.pone.0245280. eCollection 2021.
rfaRm is an R package providing a client-side interface for the Rfam database of non-coding RNA and other structured RNA elements. The package facilitates the search of the Rfam database by keywords or sequences, as well as the retrieval of all available information about specific Rfam families, such as member sequences, multiple sequence alignments, secondary structures and covariance models. By providing such programmatic access to the Rfam database, rfaRm enables genomic workflows to incorporate information about non-coding RNA, whose potential cannot be fully exploited just through interactive access to the database. The features of rfaRm are demonstrated by using it to analyze the SARS-CoV-2 genome as an example case.
rfaRm 是一个 R 包，为非编码 RNA 和其他 RNA 结构元件的 Rfam 数据库提供了一个客户端接口。该软件包可以通过关键词或序列方便地搜索 Rfam 数据库，以及检索有关特定 Rfam 家族的所有可用信息，例如成员序列、多序列比对、二级结构和协方差模型。通过为 Rfam 数据库提供这种编程访问，rfaRm 使得基因组工作流程能够整合非编码 RNA 的信息，而仅仅通过对数据库的交互式访问，是无法充分利用非编码 RNA 的潜力的。我们将使用它来分析 SARS-CoV-2 基因组作为一个示例案例，来说明 rfaRm 的功能。
