Skip to contents

Translate a nucleotide sequence to a protein sequence

Source: R/translation.R
get_translation.Rd

Translates a nucleotide sequence into a single-letter amino acid string using EXTENDED_GENETIC_CODE. Supports all IUPAC degenerate nucleotide codes. Codons containing "#" are translated as "#" (gap indicator used in some CoNGA input files). Codons not found in the extended code are translated as "X".

Usage

get_translation(seq, frame = "+1")

Arguments

seq

Character string. The nucleotide sequence to translate. May contain standard or IUPAC-degenerate bases and may be any case (converted to lowercase internally after offset trimming).

frame

Character string of length 1. Reading frame, e.g. "+1", "+2", "+3" for forward strand, or "-1", "-2", "-3" for reverse-complement strand. The sign determines strand and the absolute integer value (1, 2, or 3) determines the 0-based offset into the sequence before translation begins.

Value

A character string of amino acids. Length is floor((nchar(seq) - offset) / 3).

Examples

# Translate from frame +1 (no offset)
get_translation("ATGAAATTT", "+1")  # "MKF"
#> [1] "MKF"

# Frame +2 skips the first nucleotide
get_translation("AATGAAATTT", "+2")  # "MKF"
#> [1] "MKF"