Hi all!
Is there any way to map a short peptide sequence from virus (10-15 aa) to its corresponding genomic position?
Hi all!
Is there any way to map a short peptide sequence from virus (10-15 aa) to its corresponding genomic position?
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
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.
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
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Yes. I tried TblastN but again output is generated at protein level and not at nucleotide level.