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Modstrings: working with modified nucleotide sequences

R-CMD-check-bioc-devel BioC Build codecov BioC Years

RNA are usually in some form post-transcriptionally modified. Most prominent examples are of course rRNA and tRNA, but in recent years mRNA was also discovered to be post-transcriptionally modified.

In many resources, like the tRNAdb (Juehling et al. 2009) or the modomics database (Boccaletto et al. 2018), a dictionary for modified nucleotides was published. However, in the Bioconductor universe these information were not directly accessible or representable, since they rely extensively on special characters in the RNA modification alphabet.

Therefore, theModstrings package implements the ModRNAString class by extending the BString class from the Biostrings (Pages et al.) package. It can store RNA sequences containing special characters of the RNA modification alphabet and thus can store location and identity of modifications. Functions for conversion to a tabular format are implemented as well. A ModDNAString class is implemented analogously, which is based on the DNA modification alphabet from the Hoffman lab (Sood et al.).

The implemented classes inherit most of the functions from the parental BString class and it derivatives, which allows them to behave like the normal XString classes within the bioconductor universe.

Installation

The current version of the Modstrings package is available from Bioconductor.

# Installation
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Modstrings")
# Load and attach the package
library("Modstrings")

Literature

  • Jühling, Frank; Mörl, Mario; Hartmann, Roland K.; Sprinzl, Mathias; Stadler, Peter F.; Pütz, Joern (2009): "TRNAdb 2009: Compilation of tRNA Sequences and tRNA Genes." Nucleic Acids Research 37 (suppl_1): D159–D162. doi:10.1093/nar/gkn772.
  • Boccaletto, Pietro; Machnicka, Magdalena A.; Purta, Elzbieta; Piatkowski, Pawel; Baginski, Blazej; Wirecki, Tomasz K. et al. (2018): "MODOMICS: a database of RNA modification pathways. 2017 update." Nucleic Acids Res. 46 (D1), D303-D307. doi:10.1093/nar/gkx1030.
  • Pagès, H.; Aboyoun, P.; Gentleman, R.; DebRoy, S. (2018). "Biostrings: Efficient manipulation of biological strings." R package version 2.50.1.
  • Sood, Ankur Jai, Coby Viner, and Michael M. Hoffman. 2019. “DNAmod: The Dna Modification Database.” Journal of Cheminformatics 11 (1):30. doi:10.1186/s13321-019-0349-4.