rfaRm

rfaRm is an R package that serves as a client-side interface for the Rfam database, focusing on non-coding RNA and other structured RNA elements. This package allows users to search the Rfam database using keywords or sequences and retrieve comprehensive information about specific Rfam families. This information includes member sequences, multiple sequence alignments, secondary structures, and covariance models. By offering programmatic access to the Rfam database, rfaRm facilitates the integration of non-coding RNA information into genomic workflows.

Topic

Functional, regulatory and non-coding RNA;Nucleic acid structure analysis;Phylogenetics;Transcription factors and regulatory sites;Gene and protein families

Detail

  • Operation: Data retrieval;RNA structure covariance model generation;Multiple sequence alignment;Phylogenetic analysis

  • Software interface: Library,Command-line tool

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.14.0

  • Credit: The ERA CoBioTech UKRI/BBSRC project SyCoLim, Biotechnology and Biological Sciences Research Council (BBSRC), EPSRC Fellowship for Growth, Engineering and Phyisical Sciences Research Council.

  • Input: -

  • Output: -

  • Contact: Lara Selles Vidal lara.selles@oist.jp, Rafael Ayala rafael.ayala@oist.jp

  • Collection: -

  • Maturity: Stable

Publications

  • rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families.
  • Sellés Vidal L, et al. rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families. rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families. 2021; 16:e0245280. doi: 10.1371/journal.pone.0245280
  • https://doi.org/10.1371/JOURNAL.PONE.0245280
  • PMID: 33449976
  • PMC: PMC7810343

Download and documentation

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