back-propogation of protein motif n

[ambarishK]

Hi

Please send me code snippet to back-translate protein motif and print all possible nucleotide sequences to code the given motif.

[jfjlaros]

I am afraid you are in the wrong place. This project deals with back translations of variants, not of protein sequences.

You might have more luck with Backtranseq.

[jkvis]

Maybe something like this (untested):

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


def back_translate(protein, dna='', pos=0):
    if pos >= len(protein):
        yield dna
    else:
        for codon in sorted(CODONS[protein[pos]]):
            yield from back_translate(protein, dna + codon, pos + 1)


if __name__ == '__main__':
    for dna in back_translate('TEST'):
        print(dna)

[ambarishK]

Yes. I got it.

Many many thanks. Drop me your email-Id. It is good to share code resources for tool development.

My one is

1. [email protected]

2. [email protected]