如何在没有 BioPython 库的情况下将 RNA 翻译成蛋白质

Question

Is there any easy way to convert protein to RNA by using a dictionary and .replace function?

Also, I have no idea how to code all possible variants of the RNA and DNA code redundancy, which makes it possible to code one amino-acid, by the different RNA triplets.

I think, maybe it should be like that:

RNA = input("")
RNA_dictionary = {
  "GCA":"A", "GCC":"A", "GCG":"A", "GCU":"A",
  "UGC":"C", "UGU":"C", "GAC":"D", "GAU":"D",
  "GAA":"E", "GAG":"E", "UUC":"F", "UUU":"F",
  "GGA":"G", "GGC":"G", "GGG":"G", "GGU":"G",
  "CAC":"H", "CAU":"H", "AUA":"I", "AUC":"I",
  "AUU":"I", "AAA":"K", "AAG":"K", "UUA":"L",
  "UUG":"L", "CUA":"L", "CUC":"L", "CUG":"L",
  "CUU":"L", "AUG":"M", "AAC":"N", "AAU":"N",
  "CCA":"P", "CCC":"P", "CCG":"P", "CCU":"P",
  "CAA":"Q", "CAG":"Q", "AGA":"R", "AGG":"R",
  "CGA":"R", "CGC":"R", "CGU":"R", "CGG":"R",
  "AGC":"S", "AGU":"S", "UCA":"S", "UCC":"S",
  "UCG":"S", "UCU":"S", "ACA":"T", "ACC":"T",
  "ACG":"T", "ACU":"T", "GUA":"V", "GUC":"V",
  "GUG":"V", "GUU":"V", "UGG":"W", "UAC":"Y",
  "UAU":"Y", "UAG":"!", "UAA":"!", "UGA":"!"
}

reverse_translation = RNA_dictionary.replace #(Have no idea how to insert here the input RNA)
print (reverse_translation)

I know it all can be done by using just one function, from the BioPython. And maybe my way of learning bioinformatics and how to code in common is a bit weird. But this way I like and feel that I more really understand how the code works than just memorizing it like a poem.

Answer 1

You can use the keys of your dictionary to create a regular expression for finding the triplets. Then use the dictionary in the re.sub callback function to make the replacements:

regex = "|".join(RNA_dictionary.keys())
translation = re.sub(regex, lambda m: RNA_dictionary[m.group()], RNA)

print(translation)

Answer 2

Once you inverted your dict with the inv_dict = {v: k for k, v in ini_dict.items()} you mentioned you can use this.

seq=""
for aa in prot:
    codon = inv_dict.get(aa)
    seq+=codon

print(seq)

It doesn't account for the redundancy, but keep in mind that even for a very small protein sequence, there are thousands of possible nucleotide sequences.

For example, for the protein sequence:

AlaProLysPheTrpIleCysAla

you have 6 * 4 * 2 * 2 * 1 * 3 * 2 * 4 = 2304 possible sequences.