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1 vote

Comparing sequence similarity of two sets of peptide sequences?

After more search, I go for blastp-short with MHC peptides as query and my full-length proteins as database. Please share if you think it has problems.
Johnny Tam's user avatar
2 votes

Comparing sequence similarity of two sets of peptide sequences?

I would suggest focusing on short k-mers if you are using very small sequences. Simply quantify the similarity of the k-mer profile of each relevant pair of peptides. There are many tools for ...
Maximilian Press's user avatar
3 votes

Comparing sequence similarity of two sets of peptide sequences?

Not sure what is the shortest peptide one can fish out with LAST out of small protein database (well, it starts with protein FASTA file), but you may check out LAST ...
darked89's user avatar
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