Greetings!

I'm using Diamond to do translated alignment of a gut microbiome metagenomic sequence dataset agains the human proteome (looking for possible sequence homology and autoantigens).

Question: Diamond seems to only report alignments for sequences of read length more than 51 DNA bps or 17 amino acids. Is there a way to lower this threshold, or is there another method I should try? Ideally I'd like to align sequences of as short as 9 amino acids (approximately the length of peptides presented by MHC).

Best,

Sherman