Structstrings package implements the widely used to bracket
annotation for storing base pairing information in structured RNA. For
example it is used in the ViennaRNA package (Lorenz et al. 2011), the
tRNAscan-SE software (Lowe et al. 1997) and the tRNAdb (Jühling et al. 2009).
Structstrings uses the infrastructure provided by the
Biostrings package and derives the class
DotBracketString and such from the equivalent
BString class. From these base pair table can be produced for
in depth analysis. For this purpose the
class is derived from the
DataFrame class. In addition the loop
IDs of the base pairs can be retrieved as a
derivate if the
IntegerList. Generally, it checks automatically
for the validity of the dot bracket annotation.
The conversion of the
DotBracketString to the base pair table
and the loop indices is implemented in C for efficiency. The C implementation
to a large extent inspired by the
This package was developed as a requirement for the
However, other projects might benefit as well, so it was split of and
Please refer to the Structstrings vignette for an example how to work and use the package: Structstrings.
Felix G M Ernst [aut,cre]
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.
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