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Map cached MODOMICS modifications onto reference sequences

Source: R/modomics.R
modomics_mods.Rd

Uses bundled MODOMICS data to map known tRNA modification positions onto user-provided reference sequences using pairwise alignment. No internet connection is required for organisms included in the package (see modomics_organisms()). For other organisms, falls back to fetch_modomics_mods().

Usage

modomics_mods(fasta, organism, 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").

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/trna_only.fa.gz")
modomics_mods(fa, "Escherichia coli")
#> Processing 182 MODOMICS sequences.
#> Matching MODOMICS sequences to reference FASTA.
#> Found 698 modification annotations.
#> # A tibble: 698 × 4
#>    ref                     pos mod_full                 mod1 
#>    <chr>                 <int> <chr>                    <chr>
#>  1 host-tRNA-Ala-TGC-1-1    17 dihydrouridine           D    
#>  2 host-tRNA-Ala-TGC-1-1    34 uridine 5-oxyacetic acid cmo5U
#>  3 host-tRNA-Ala-TGC-1-1    46 7-methylguanosine        m7G  
#>  4 host-tRNA-Ala-TGC-1-1    54 5-methyluridine          m5U  
#>  5 host-tRNA-Ala-TGC-1-1    55 pseudouridine            Y    
#>  6 host-tRNA-Ala-GGC-1-1    17 dihydrouridine           D    
#>  7 host-tRNA-Ala-GGC-1-1    46 7-methylguanosine        m7G  
#>  8 host-tRNA-Ala-GGC-1-1    54 5-methyluridine          m5U  
#>  9 host-tRNA-Ala-GGC-1-1    55 pseudouridine            Y    
#> 10 host-tRNA-Arg-ACG-1-1     8 4-thiouridine            s4U  
#> # ℹ 688 more rows
# }