GRangestRNAdbImport 1.24.0
The tRNAdb and mttRNAdb (Jühling et al. 2009) is a compilation of tRNA sequences and tRNA genes. It is a follow up version of the database of Sprinzl et al. (Sprinzl and Vassilenko 2005).
Using tRNAdbImport the tRNAdb can be accessed as outlined on the website
http://trna.bioinf.uni-leipzig.de/ and the results
are returned as a GRanges object.
The tRNAdb Server is currently not available. Some chunks of the code in this vignette are currently not avilable. See https://www.bioinf.uni-leipzig.de/services/webservices for more information.
GRangeslibrary(tRNAdbImport)# accessing tRNAdb
# tRNA from yeast for Alanine and Phenylalanine
gr <- import.tRNAdb(organism = "Saccharomyces cerevisiae",
aminoacids = c("Phe","Ala"))## Warning: tRNAdb Server seems to be not available.# get a Phenylalanine tRNA from yeast
gr <- import.tRNAdb.id(tdbID = gr[gr$tRNA_type == "Phe",][1L]$tRNAdb_ID)# find the same tRNA via blast
gr <- import.tRNAdb.blast(blastSeq = gr$tRNA_seq)# accessing mtRNAdb
# get the mitochrondrial tRNA for Alanine in Bos taurus
gr <- import.mttRNAdb(organism = "Bos taurus",
aminoacids = "Ala")## Warning: tRNAdb Server seems to be not available.# get one mitochrondrial tRNA in Bos taurus.
gr <- import.mttRNAdb.id(mtdbID = gr[1L]$tRNAdb_ID)# check that the result has the appropriate columns
istRNAdbGRanges(gr)## Warning: Input GRanges object does not meet the requirements of the function. The following columns are expected:
## 'tRNA_length', 'tRNA_type', 'tRNA_anticodon', 'tRNA_seq', 'tRNA_str', 'tRNA_CCA.end', 'tRNAdb_ID', 'tRNAdb', 'tRNAdb_organism', 'tRNAdb_strain', 'tRNAdb_taxonomyID', 'tRNAdb_verified'.## [1] FALSEGRanges from the RNA databaseThe tRNAdb offers two different sets of data, one containing DNA sequences and
one containing RNA sequences. Depending on the database selected, DNA as
default, the GRanges will contain a DNAStringSet or a ModRNAStringSet as
the tRNA_seq column. Because the RNA sequences can contain modified
nucleotides, the ModRNAStringSet class is used instead of the RNAStringSet
class to store the sequences correctly with all information intact.
gr <- import.tRNAdb(organism = "Saccharomyces cerevisiae",
aminoacids = c("Phe","Ala"),
database = "RNA")
gr$tRNA_seqThe special characters in the sequence might no exactly match the ones shown on
the website, since they are sanitized internally to a unified dictionary defined
in the Modstrings package. However, the type of modification encoded will
remain the same (See the Modstrings package for more details).
The information on the position and type of the modifications can also be
converted into a tabular format using the separate function from the
Modstrings package.
separate(gr$tRNA_seq)The output can be saved or directly used for further analysis.
library(Biostrings)
library(rtracklayer)
# saving the tRAN sequences as fasta file
writeXStringSet(gr$tRNA_seq, filepath = tempfile())
# converting tRNAdb information to GFF compatible values
gff <- tRNAdb2GFF(gr)
gff
# Saving the information as gff3 file
export.gff3(gff, con = tempfile())Please have a look at the tRNA package for further analysis of the tRNA
sequences.
sessionInfo()## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
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## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
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## other attached packages:
## [1] rtracklayer_1.66.0 tRNAdbImport_1.24.0 tRNA_1.24.0
## [4] Structstrings_1.22.0 Modstrings_1.22.0 Biostrings_2.74.0
## [7] XVector_0.46.0 GenomicRanges_1.58.0 GenomeInfoDb_1.42.0
## [10] IRanges_2.40.0 S4Vectors_0.44.0 BiocGenerics_0.52.0
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## [5] bslib_0.8.0 ggplot2_3.5.1
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## [63] glue_1.8.0 BiocManager_1.30.25
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## [67] R6_2.5.1 MatrixGenerics_1.18.0
## [69] GenomicAlignments_1.42.0 zlibbioc_1.52.0Jühling, Frank, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, and Joern Pütz. 2009. “TRNAdb 2009: Compilation of tRNA Sequences and tRNA Genes.” Nucleic Acids Research 37: D159–D162. https://doi.org/10.1093/nar/gkn772.
Sprinzl, Mathias, and Konstantin S. Vassilenko. 2005. “Compilation of tRNA Sequences and Sequences of tRNA Genes.” Nucleic Acids Research 33: D139–D140. https://doi.org/10.1093/nar/gki012.