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.
Modstrings package implements the
ModRNAString class by
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 analogous, which
is based on the DNA modification alphabet from the Hoffman lab (Sood et
The implemented classes inherit most of the functions from the parental
BString class and it derivatives, which allows them to behave like the
XString classes within the bioconductor universe.
The current version of the
Modstrings package is available from
# Installation if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Modstrings") # Load and attach the package library("Modstrings")
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