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peptide to genomic cordinates mapping

Hi all!

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

sequence genome alignment
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written by rajmandage • rajmandage

3 answers

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

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written by agata88 agata88

did you try tblastn?

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written by ssv.bio ssv.bio

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

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written by rajmandage • 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.

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written by rajmandage • rajmandage

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.

• 1 views • link
written by agata88 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

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written by agata88 agata88

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