How to get nucleotidic sequence from a protein fasta file?

Question

[Luis999]

Hello, have a nice day everyone. Excuse me, I have a question that I've been stuck on for a long time, the case I have is the following.

From a transcriptome of a multi fasta file, I translate the longest orf to obtain putative peptides, now I have to map these putatives to the genome of the same organism from which the transcript was obtained, for that, due to the process that I am going to use, I need the corresponding nucleotide sequence to the peptides I got by translating the longest orf. Does anyone know of a method where I can do this reverse translation with a custom query? I know that there are many pages on the internet to do reverse translation, but in these cases I have to type a query from their databases, and I can't put the millions of sequences in my fasta file.

Answer 1

[lieven.sterck]

not sure I understand your question/issue fully, but back-translating a protein to its nucleotide sequence is nearly impossible (explaining why will take us back to basic molecular biology)

You can however align your protein sequence "directly" to the genome, for instance by using tBLASTn .

Alternatively, can't you keep track of the nucleotide sequence you initially made the translation to protein from and then use that nucleotide sequence in your search?

[Mensur Dlakic]

explaining why will take us back to basic molecular biology

My suggestion to the poster is to search Biostars for codon degeneracy, and it will be explained in one of many posts. Maybe try the same search with Google.

[lieven.sterck]

that is indeed the keyword of importance here :)