1 Introduction

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.

2 Importing as GRanges

library(tRNAdbImport)

# accessing tRNAdb
# tRNA from yeast for Alanine and Phenylalanine
gr <- import.tRNAdb(organism = "Saccharomyces cerevisiae",
              aminoacids = c("Phe","Ala"))

# get a Phenylalanine tRNA from yeast
gr <- import.tRNAdb.id(tdbID = gr[gr$tRNA_type == "Phe",][1]$tRNAdb_ID)

# find the same tRNA via blast
gr <- import.tRNAdb.blast(blastSeq = gr$tRNA_seq)

## Warning: The result potentially contains modified DNA and RNA nucleotides.
## Downstream analysis might be limited.

# accessing mtRNAdb
# get the mitochrondrial tRNA for Alanine in Bos taurus
gr <- import.mttRNAdb(organism = "Bos taurus", 
                      aminoacids = "Ala")

# get one mitochrondrial tRNA in Bos taurus. 
gr <- import.mttRNAdb.id(mtdbID = gr[1]$tRNAdb_ID)

# check that the result has the appropriate columns
istRNAdbGRanges(gr)

## [1] TRUE

3 Further analysis

The output can be saved or directly used for further analysis.

library(Biostrings)
library(rtracklayer)
writeXStringSet(gr$tRNA_seq, filepath = tempfile())
gff <- tRNAdb2GFF(gr)
export.gff3(gff, con = tempfile())

Please have a look at the tRNA package for further analysis of the tRNA sequences.

4 Session info

sessionInfo()

## R version 3.5.1 Patched (2018-07-12 r74967)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.5 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.8-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.8-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] rtracklayer_1.42.0   Biostrings_2.50.0    XVector_0.22.0      
##  [4] tRNAdbImport_1.0.0   tRNA_1.0.0           GenomicRanges_1.34.0
##  [7] GenomeInfoDb_1.18.0  IRanges_2.16.0       S4Vectors_0.20.0    
## [10] BiocGenerics_0.28.0  BiocStyle_2.10.0    
## 
## loaded via a namespace (and not attached):
##  [1] Biobase_2.42.0              httr_1.3.1                 
##  [3] assertive.sets_0.0-3        assertthat_0.2.0           
##  [5] assertive.data_0.0-1        BiocManager_1.30.3         
##  [7] GenomeInfoDbData_1.2.0      Rsamtools_1.34.0           
##  [9] yaml_2.2.0                  pillar_1.3.0               
## [11] backports_1.1.2             lattice_0.20-35            
## [13] glue_1.3.0                  assertive.data.uk_0.0-2    
## [15] assertive.matrices_0.0-1    digest_0.6.18              
## [17] assertive.types_0.0-3       colorspace_1.3-2           
## [19] htmltools_0.3.6             Matrix_1.2-14              
## [21] plyr_1.8.4                  XML_3.98-1.16              
## [23] pkgconfig_2.0.2             assertive.data.us_0.0-2    
## [25] assertive.properties_0.0-4  assertive.reflection_0.0-4 
## [27] bookdown_0.7                zlibbioc_1.28.0            
## [29] purrr_0.2.5                 scales_1.0.0               
## [31] assertive_0.3-5             BiocParallel_1.16.0        
## [33] tibble_1.4.2                ggplot2_3.1.0              
## [35] SummarizedExperiment_1.12.0 assertive.code_0.0-3       
## [37] lazyeval_0.2.1              magrittr_1.5               
## [39] crayon_1.3.4                assertive.strings_0.0-3    
## [41] evaluate_0.12               assertive.numbers_0.0-2    
## [43] xml2_1.2.0                  tools_3.5.1                
## [45] matrixStats_0.54.0          assertive.files_0.0-2      
## [47] stringr_1.3.1               munsell_0.5.0              
## [49] DelayedArray_0.8.0          bindrcpp_0.2.2             
## [51] compiler_3.5.1              rlang_0.3.0.1              
## [53] grid_3.5.1                  RCurl_1.95-4.11            
## [55] assertive.models_0.0-2      assertive.base_0.0-7       
## [57] bitops_1.0-6                rmarkdown_1.10             
## [59] gtable_0.2.0                codetools_0.2-15           
## [61] curl_3.2                    assertive.datetimes_0.0-2  
## [63] R6_2.3.0                    GenomicAlignments_1.18.0   
## [65] knitr_1.20                  dplyr_0.7.7                
## [67] bindr_0.1.1                 rprojroot_1.3-2            
## [69] stringi_1.2.4               Rcpp_0.12.19               
## [71] tidyselect_0.2.5            xfun_0.4