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

Author

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  • Lara Sellés Vidal
  • Rafael Ayala
  • Guy-Bart Stan
  • Rodrigo Ledesma-Amaro

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.

Suggested Citation

  • Lara Sellés Vidal & Rafael Ayala & Guy-Bart Stan & Rodrigo Ledesma-Amaro, 2021. "rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families," PLOS ONE, Public Library of Science, vol. 16(1), pages 1-13, January.
    • Handle: RePEc:plo:pone00:0245280
    DOI: 10.1371/journal.pone.0245280
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