The 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 DotBracketString and
related classes from the BString class. From these base pair tables can be
produced for in depth analysis, for which the DotBracketDataFrame class
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 IntegerList
class. Generally, all classes check automatically for the validity of the base
pairing information.
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
Bioconductor.
# 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.
- Lorenz, Ronny; Bernhart, Stephan H.; Höner zu Siederdissen, Christian; Tafer, Hakim; Flamm, Christoph; Stadler, Peter F.; Hofacker, Ivo L. (2011): "ViennaRNA Package 2.0". Algorithms for Molecular Biology 6:26. doi:10.1186/1748-7188-6-26
- Lowe, T.M.; Eddy, S.R.(1997): "tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence". Nucl. Acids Res. 25: 955-964. doi:10.1093/nar/25.5.955
- 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.
- Pagès, H.; Aboyoun, P.; Gentleman, R.; DebRoy, S. (2018). "Biostrings: Efficient manipulation of biological strings." R package version 2.50.1.
