Protein sequence to Nucleotide sequence

Question

[mittu1602]

Hello All,

I have file1 with protein sequence and another file with its respective decoded nucl codon sequence, is there any one liner which looks for aa single letter in file2 - change the protein sequence to the nucleotide sequence and save it as a file 3.

For eg:

File1.fasta

MFLILLISLPTAFAVIGDLKCTTVSINDVDTGVPSIST.....................

File2.txt (tab file)

M ATG

F TTT

.. ...

Expected output

file3.fasta

ATGTTTTGATACTTT....................

Answer 1

[Pierre Lindenbaum]

backtranseq http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/backtranseq.html

backtranseq reads a protein sequence and writes the nucleic acid sequence it is most likely to have come from.

Answer 2

[5heikki]

This is not very efficient, but it does work (notice, these files do not have headers)..

cat file.aa
MFLILLI

cat file.map
M       AAA
F       TTT
L       CCC
I       GGG

for x in $(fold -w 1 file.aa); do awk -v x="$x" 'BEGIN{FS="\t"}{if($1==x){printf $2}}' file.map; done
AAATTTCCCGGGCCCCCCGGG

But surely you are aware that it's impossible to go from aa sequence back to the original nt sequence? E.g. six different codons encode Leucine..