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Fetch tRNA modification annotations from MODOMICS

Source: R/modomics.R
fetch_modomics_mods.Rd

Downloads tRNA modification data from the MODOMICS database and maps modification positions onto user-provided reference sequences using pairwise alignment.

Usage

fetch_modomics_mods(fasta, organism, cache_dir = NULL, min_identity = 0.7)

Arguments

fasta

Path to a FASTA file or a Biostrings::DNAStringSet object containing reference tRNA sequences.

organism

Character string specifying the organism name as used in MODOMICS (e.g., "Saccharomyces cerevisiae", "Escherichia coli").

cache_dir

Optional directory path for caching API responses as RDS files. If NULL (default), no caching is performed.

min_identity

Minimum alignment identity (0–1) required to accept a match between a MODOMICS sequence and a reference sequence. Default 0.7.

Value

A tibble with columns:

  • ref: reference sequence name from the FASTA

  • pos: 1-based position in the reference sequence

  • mod_full: full modification name (e.g., "1-methyladenosine")

  • mod1: short modification name (e.g., "m1A")

Examples

# \donttest{
fa <- clover_example("ecoli/validated.fa.gz")
mods <- fetch_modomics_mods(fa, "Escherichia coli")
#> Fetching MODOMICS modification dictionary.
#> Fetching MODOMICS tRNA sequences for "Escherichia coli".
#> Processing 182 MODOMICS sequences.
#> Matching MODOMICS sequences to reference FASTA.
#> Found 695 modification annotations.
mods
#> # A tibble: 695 × 4
#>    ref                     pos mod_full                 mod1 
#>    <chr>                 <int> <chr>                    <chr>
#>  1 host-tRNA-Ala-TGC-1-1    41 dihydrouridine           D    
#>  2 host-tRNA-Ala-TGC-1-1    58 uridine 5-oxyacetic acid cmo5U
#>  3 host-tRNA-Ala-TGC-1-1    70 7-methylguanosine        m7G  
#>  4 host-tRNA-Ala-TGC-1-1    78 5-methyluridine          m5U  
#>  5 host-tRNA-Ala-TGC-1-1    79 pseudouridine            Y    
#>  6 host-tRNA-Ala-GGC-1-1    41 dihydrouridine           D    
#>  7 host-tRNA-Ala-GGC-1-1    70 7-methylguanosine        m7G  
#>  8 host-tRNA-Ala-GGC-1-1    78 5-methyluridine          m5U  
#>  9 host-tRNA-Ala-GGC-1-1    79 pseudouridine            Y    
#> 10 host-tRNA-Arg-ACG-1-1    32 4-thiouridine            s4U  
#> # ℹ 685 more rows
# }