How to get nucleotidic sequence from a protein fasta file?
1
0
Entering edit mode
2.0 years ago
Luis999 ▴ 20

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.

biopython fasta python • 615 views
ADD COMMENT
0
Entering edit mode
2.0 years ago

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?

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

that is indeed the keyword of importance here :)

ADD REPLY

Login before adding your answer.

Traffic: 1628 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6