Finding unique regions in a sequence

[ramirob]

I have a sequence and would like to find unique regions (when compared to a human database) within it that are at least 11 amino acids long. Any leads on how to address this?

My current thinking is to use blast to the human protein database and find region(s) that have no similarity to any other sequence, but I am wondering if there are other, more principled ways.

Ultimately, the goal is to find a unique region so one can design an antibody that would be specific to the protein.

[Masklin]

I don't know of any existing softwares that does this. I would split your sequence into all its possible 11-mers, and for each of those search through the human h38.faa file, split into entries (proteins) if you have the CPU cores for it. Might take a long time.