Structstrings package implements the widely used dot bracket annotation for
storing base pairing information in structured RNA. For example it is heavily
used in the ViennaRNA (Lorenz et al. 2011) package, the tRNAscan-SE
(Lowe et al. 1997) software and the tRNAdb
(Juehling et al. 2009).
Structstrings uses the infrastructure provided by the
Biostrings package and derives the class
related classes from the
BString class. From these base pair tables can be
produced for in depth analysis, for which the
is derived from the
DataFrame class. In addition, the loop indices of the base
pairs can be retrieved as a
LoopIndexList, a derivate of the
class. Generally, all classes check automatically for the validity of the base
The conversion of the
DotBracketString to the base pair table and the loop
indices is implemented in C for efficiency. The C implementation is inspired
by the ViennaRNA package to a large extent.
This package was developed as an improvement for the
tRNA package. However,
other projects might benefit as well, so it was split of and improved upon.
The current version of the
Structstrings package is available from
# Installation if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Structstrings") # Load and attach the package library("Structstrings")
Please have a look at vignette for details on the provided functions.
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