Map identity elements to tRNA sequence positions — map_identity_to

Converts Sprinzl positions in identity element data to 1-based sequence positions for a specific tRNA, enabling overlay on structure plots via the outlines parameter of plot_tRNA_structure().

Usage

map_identity_to_trna(elements, sprinzl_coords, trna_id)

Arguments

elements: A tibble of identity elements as returned by identity_elements().
sprinzl_coords: A tibble of Sprinzl coordinates as returned by read_sprinzl_coords().
trna_id: Character string identifying the tRNA to map (must match a trna_id value in sprinzl_coords).

Value

The input elements tibble with an added pos column containing the 1-based sequence position. Rows where the Sprinzl position does not exist in the target tRNA (including His G\(_{-1}\) at sprinzl_pos = -1 and structural determinants with sprinzl_pos = NA) are dropped.

Examples

coords <- read_sprinzl_coords(
  clover_example("sprinzl/sacCer_global_coords.tsv.gz")
)
elems <- identity_elements(
  "Saccharomyces cerevisiae",
  amino_acid = "Ala"
)
map_identity_to_trna(elems, coords, "nuc-tRNA-Ala-AGC-1-1")
#> # A tibble: 5 × 13
#>   amino_acid domain  sprinzl_pos nucleotide region       type  strength pair_pos
#>   <chr>      <chr>         <int> <chr>      <chr>        <chr> <chr>       <int>
#> 1 Ala        Eukarya          73 A          discriminat… dete… strong         NA
#> 2 Ala        Eukarya           3 G          acceptor_st… dete… strong         70
#> 3 Ala        Eukarya          70 U          acceptor_st… dete… strong          3
#> 4 Ala        Eukarya           3 G          acceptor_st… anti… NA             70
#> 5 Ala        Eukarya          70 U          acceptor_st… anti… NA              3
#> # ℹ 5 more variables: pair_type <chr>, against_aars <chr>, universal <lgl>,
#> #   description <chr>, pos <dbl>