I have a project to write in Python that requires to write a function that given degenerate DNA sequence (for example: KKGTACACCAG) sequence and a molecular weight interval, returns a list of all unambiguous sequences represented by the given sequence (encoding based on IUPAC alphabet: http://www.bioinformatics.org/sms/iupac.html).

Is there any function in Biopython to convert a DNA sequence from degenerate to unambiguous base pairs?

Also, Is it possible to use the molecular weight function from Bio.SeqUtils library for an ambiguous DNA?


2 Answers 2

from Bio.Seq import Seq
coding_dna = Seq("AAYGANAGYCARAGYAAR")

This gives


So .translate() will read a degenerate code and provide the unambiguous amino acid, except where it is unable to do so e.g. GAN because this is a split between asp and glu. Thus GAR or GAY is fine, but GAN gives X

You would then use itertools by mapping (map) against the triplet code (import Bio.Data.CodonTable) to obtain all permutations. Doesn't work for X admittedly and stop codons a special case (3 possibilities).

Bio.Data.CodonTable.list_possible_proteins would solve the X problem, but stop codons remain a special case.

I seriously did like the Stackoverflow link in the comments, with the double map funtion ... very slick.

  • 1
    $\begingroup$ I am missing the SO link the one with : the double map funtion ... , could you add it to your answer $\endgroup$
    – pippo1980
    Jul 14, 2023 at 17:20
  • $\begingroup$ @pippo1980ONSTRIKE I can't do it now, but I'll look at it early next week. Please check the answer below from acvill $\endgroup$
    – M__
    Jul 14, 2023 at 17:23
  • 1
    $\begingroup$ cheers, but R is like ancient greek to me, I am following this question though $\endgroup$
    – pippo1980
    Jul 14, 2023 at 17:28

M__'s approach is good, but, as explained, some subset of the unambiguous DNA sequences will not be recovered because of the ambiguity in reverse-translation due to the degeneracy of the genetic code. I don't know a python approach, but here's an R function that returns a vector of all the possible unambiguous DNA strings:

make_unambiguous <- function(dna) {
  iupac <- tibble(code = c("A", "C", "G", "T",
                           "R", "Y", "S", "W",
                           "K", "M", "B", "D",
                           "H", "V", "N"),
                  base = c("A", "C", "G", "T",
                           "AG", "CT", "GC", "AT",
                           "GT", "AC", "CGT", "AGT",
                           "ACT", "ACG", "ACGT"))

  tibble(dna) |>
    separate_rows(dna, sep = '(?<=.)(?=.)') |>
    left_join(iupac, by = c("dna" = "code")) |>
    pull(base) |>
    str_split("") |>
    expand.grid(stringsAsFactors = FALSE) |>
    unite(col = sequence, sep = "") |>

make_unambiguous(dna = "AAYGANAGYCARAGYAAR")

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