Name Mode Size
.github 040000
R 040000
data 040000
inst 040000
man 040000
pkgdown 040000
src 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 0 kb
DESCRIPTION 100644 2 kb
NAMESPACE 100644 2 kb
NEWS 100644 0 kb 100644 3 kb
# Structstrings: implementation of the dot bracket annotations with Biostrings <img src="" height="300" align="right"> <!-- badges: start --> [![R-CMD-check](]( [![BioC Build](]( [![codecov](]( [![BioC Years](]( <!-- badges: end --> 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](#Literature)) package, the tRNAscan-SE ([Lowe et al. 1997](#Literature)) software and the tRNAdb ([Juehling et al. 2009](#Literature)). `Structstrings` uses the infrastructure provided by the [Biostrings](#Literature) 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. ```{r} # 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.