Structstrings: Structstrings: implementation of the dot bracket annotations...
In FelixErnst/Structstrings: Implementation of the dot bracket annotations with Biostrings
Structstrings R Documentation
Structstrings: implementation of the dot bracket annotations with
Biostrings
Description
The 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 DotBracketDataFrame
class is derived from the DataFrame class. In addition the loop
IDs of the base pairs can be retrieved as a LoopIndexList, 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
ViennaRNA package.
This package was developed as a requirement for the tRNA package.
However, other projects might benefit as well, so it was split of and
improved upon.
Manual
Please refer to the Structstrings vignette for an example how to work and
use the package: Structstrings.
Author(s)
Felix G M Ernst [aut,cre]
References
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.
FelixErnst/Structstrings documentation built on Nov. 6, 2024, 12:11 a.m.
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| Structstrings | R Documentation |
Structstrings: implementation of the dot bracket annotations with Biostrings
Description
The 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 DotBracketDataFrame
class is derived from the DataFrame class. In addition the loop
IDs of the base pairs can be retrieved as a LoopIndexList, 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
ViennaRNA package.
This package was developed as a requirement for the tRNA package.
However, other projects might benefit as well, so it was split of and
improved upon.
Manual
Please refer to the Structstrings vignette for an example how to work and use the package: Structstrings.
Author(s)
Felix G M Ernst [aut,cre]
References
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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