I'd like to get some help with Blast against the protein nr database on the Galaxy server or NCBI. When I do blast in batch, the blast sequence of above 30 amino acids comes as expected but sequences less than 30 amino acid residues show all to be unique, when they are not. I know this because when I take the same shorter sequences individually and perform a blast search, it shows similarity with previously reported proteins.

Please tell me if there is any way to do parameter adjustments that I can apply to solve this issue.