DNA to protein in python

Question

[ashkan]

Hi Guys,

I have a list of DNA sequences like this: very small example:

> seq = ['ATGGCGGCGCGA', 'GCCTCTGCCTTG', 'CTGAAAACG']

and if you divide the number of characters in each sequence by 3 you would get even number. I also have this dictionary which is codons and amino acids.

gencode = {
    'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
    'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K', 'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
    'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
    'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q', 'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
    'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
    'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
    'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
    'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_', 'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W'}

I want replace each codn (3 characters) with its amino acid(its value in the above dictionary). the results for the small example would be like this:

AA : ['MAAR', 'ASAL', 'LKT']

do you guys know how to do that?

Answer 1

[WouterDeCoster]

Biopython has a translate function, so you don't have to code this yourself. Googling will help you, e.g. http://biopython.org/wiki/Seq and http://biopython.org/DIST/docs/tutorial/Tutorial.html