Closed Koeng101 closed 1 year ago
Should this be a toggleable setting, or just default behavior? Or maybe this is information that should live in the codon table?
From what I see according to NCBI:
The initiator codon - whether it is AUG, CTG, TTG or something else, - is by default translated as methionine (Met, M). The possible intiator codons are marked as 'M' in the second ('Starts') row of the translation tables.
However, it seems like cryptic Leu-tRNA mediated initiation is also a thing that happens.
My proposal: modify the Table
interface such that instead of returning a []string
of start codons, it returns a map[string]rune
of start codons to the associated amino acid. We can have this be always map to 'M'
for our default codon tables, which means a user could make an implementation that corrects this behavior.
Working on this now.
Ended up going a slightly different route of adding GetStartCodonTable
method to Table
interface to prefer extension of interface over modification.
testTranslation, _ := codon.Translate(gfpDnaSequence, codon.GetCodonTable(11))
This fails in the case of
gfpDnaSequence := "TTGGCT...TAA"
, which is perfectly valid for a start codon.