BioJulia/BioSequences.jl

Implement reverse translation (AminoAcid -> Codon)

BeastyBlacksmith opened this issue · 6 comments

BeastyBlacksmith commented

I am thinking about where a good place for the codon and aminoacid tables would be in julia and wanted to ask if it would fit in here.

Expected Behavior

convert(Vector{RNAMer{3}}, AA_A) == RNAMer{3}.(["GCU", "GCA", "GCC", "GCG"])
convert(AminoAcid, RNAMer{3}("GCU")) == AA_A

Maybe have an extra type alias const Codon = RNAMer{3}

Possible Solution / Implementation

Add two lookup tables.

Context

Could go alternatively in a separate package.

jakobnissen commented

All of this is already implemented in BioSequences.jl:

julia> using BioSequences

julia> DNACodon
Mer{DNAAlphabet{2}, 3}

julia> RNACodon
Mer{RNAAlphabet{2}, 3}

See also https://biojulia.net/BioSequences.jl/stable/transforms/#Translation-1

jakobnissen commented

Closing as resolved - if there are any features you'd want to add, you are free to comment and I'll re-open

BeastyBlacksmith commented

Indeed this works in the Codon -> AminoAcid direction, but not in the reverse direction.
I get that this is not unique and thus I'd like to get all Codons representing an amino acid.
Furthermore I'd like to do this with single codons without having to convert them to LongRNASeq

jakobnissen commented

Translation of single DNA codons is a feature in the upcoming v3, already implemented. There is no such thing as reverse translation in BioSequences. We could add that

jakobnissen commented

I added an implementation here https://github.com/jakobnissen/play/blob/master/revtrans.jl (also see the accompanying blog post).

The plan now is to wait for BioSequences v3 where kmers are moved to another repo, and then implement reverse translation in that repo.

  • 👍1
jakobnissen commented

This issue is now tracked here: BioJulia/Kmers.jl#19