rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families

PLoS One. 2021 Jan 15;16(1):e0245280. doi: 10.1371/journal.pone.0245280. eCollection 2021.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Genetic
  • Humans
  • RNA, Untranslated / chemistry
  • RNA, Untranslated / genetics*
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • SARS-CoV-2 / genetics
  • Sequence Analysis, RNA / methods*
  • Software*

Substances

  • RNA, Untranslated
  • RNA, Viral

Grants and funding

RLA, GBS and LSV acknowledge the ERA CoBioTech UKRI/BBSRC project SyCoLim (BB/T011408/1), Biotechnology and Biological Sciences Research Council (BBSRC) (https://bbsrc.ukri.org/). GBS acknowledges the EPSRC Fellowship for Growth (EP/M002187/1), Engineering and Phyisical Sciences Research Council (https://epsrc.ukri.org/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.