Structstrings: implementation of the dot bracket annotations with Biostrings

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.

Installation

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")

Functions

Please have a look at vignette for details on the provided functions.

Literature

• 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.