I would like to translate a bacterial DNA sequence into a protein using the GENETIC_CODE Id 11 (instead of the Standard Id 1) and below are the commands used:
dna <- "TTGAGGATGACGAATCGTAACGTCGAATGGACTGATAATGCCTGGGATGAATATATCTATTGGCAGACACAGGATAAAAAGATACTTAAGCGTATTAATACCTTAATCAAAGAATGTCAGCGAACACCTTTTGAAGGAACAGGAAAACCAGAACCTTTAAAAGCTAATCTTTCAGGATTTTGGAGTCGTAGGATTGATGAAAAGCATAGATTAGTTTATGAAGTGACAGATGAACGAATCTCTATAATTCAATGTCGATTCCATTACTAA" dna_obj <- DNAString(dna, start = 1) translate(dna_obj, genetic.code = getGeneticCode("11", full.search = FALSE)) 90-letter "AAString" instance seq: LRMTNRNVEWTDNAWDEYIYWQTQDKKILKRINTLIKECQRTPFEGTGKPEPLKANLSGFWSRRIDEKHRLVYEVTDERISIIQCRFHY*
The 1st residue should be a Methionine, and not a Leucine as returned by translate(). The genetic code 11 translates as M the TTG codon (and also few others) if this one is located as the 1st codon in the sequence.
See the NCBI reference genetic code for the alternative codons usage in GENETIC_CODE 11:
Am I missing a parameter/option somewhere to make the selected GENETIC_CODE work properly? or is translate() not designed to take into account the codons positions for amino-acid assignments?
ps: Thanks for making this great package available to the community!