I have a list of peptides from the Western Reserve strain of the Vaccinia virus. I wish to find sequences in the proteome of the MVA. I have tried BLAST, but it seems that the entire proteome of the MVA is not readily available. So I tried a tblastn as well, in the hopes that the genome of MVA will give results. But this did not help either, despite there being a publication wherein the entire genome of MVA has been sequenced. Any suggestions would be of great help.
Hello, first you must know what you want to compare (nucleotides or amino acids). You want to compare peptides (aa) then you should use protein blast (compare protein / protein), you can also use http://www.uniprot.org/ (the best protein database), now you can also compare protein with nucleotides ( Tblast) or transform your amino acids to nucleotides and use nucleotide blast or xblast.
Try the Vipr-Database (formerly poxvirus.org)
https://www.viprbrc.org/brc/home.spg?decorator=pox
I Agree with Gundrun, ViPR is the best and most updated database. Try to see if they have the aa ora nt sequences of your virus, then i suggest you to download the nucleotide sequence and performa tblastx with your query and a database made by fasta from the nt sequences you downloaded from vipr.
tblastx translates both to aa, it is the more sensitive.
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