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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

if (FALSE) { # \dontrun{
fa <- clover_example("ecoli/validated.fa.gz")
mods <- fetch_modomics_mods(fa, "Escherichia coli")
mods
} # }