peptide to genomic cordinates mapping

Question

[rajmandage]

Hi all!

Is there any way to map a short peptide sequence from virus (10-15 aa) to its corresponding genomic position?

Answer 1

[agata88]

Look here:

How To Map Peptides To Genomic Locations (Hg19)

I would suggest to convert your peptide to dna in fasta format and then map to virus genome.

Best,

Agata

Answer 2

[ssv.bio]

did you try tblastn?

[rajmandage]

Yes. I tried TblastN but again output is generated at protein level and not at nucleotide level.

Answer 3

[rajmandage]

Dear Agata, Thanks for the prompt reply.

The limiting factor is that I have peptide sequence retrieved from virus and my aim is to map it to virus genome. Therefore I can not go with this methodology since viruses have genomes with a distinct nucleotide composition and codon usage.

[agata88]

I found the tool that can help you, I hope:

http://www.bioinformatics.org/sms2/rev_trans.html

There is a Codon Usage Database button in which you'll be able to prepare genetic code for your virus. I don't know which virus you have, but mayby it is on that list :)

Then you can just run rev_trans and you'll have translated list of DNA sequences.

Hope it will help,

Agata

[agata88]

Why can't you use virus codons to change peptide to virus DNA? And then map to virus genome? The situation is analogical to suggestions from last post.

[rajmandage]

Thanks Agata for the details.