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Implementation of the dot bracket annotations with Biostrings

Bioconductor version: Release (3.19)

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

Author: Felix G.M. Ernst [aut, cre]

Maintainer: Felix G.M. Ernst < at>

Citation (from within R, enter citation("Structstrings")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Structstrings HTML R Script
Reference Manual PDF


biocViews Alignment, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License Artistic-2.0
Depends R (>= 4.0), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), Biostrings(>= 2.57.2)
Imports methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices
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Suggests testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
Linking To IRanges, S4Vectors
Depends On Me tRNA, tRNAdbImport
Imports Me tRNAscanImport
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Follow Installation instructions to use this package in your R session.

Source Package Structstrings_1.20.0.tar.gz
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macOS Binary (x86_64) Structstrings_1.20.0.tgz
macOS Binary (arm64) Structstrings_1.20.0.tgz
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