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 analogous, 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.
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")
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.