I was wondering if Miniprot could also be (ab)used to search for very short sequences/peptides (say, even down to 8AA) in large genomes. I successfully used the provided test data trimming the protein down to just MADTQYILP with -n 1 -l 4 -k 4. Now the weird thing is that I can't find any control peptides (fragments of Myosin or Helicases up to lengths 100) when searching against a full genome (refseq grch38 p14 in this case). Is this expected? Would adjusting parameters help and if yes, which in addition to the above?
Many thanks,
Andreas
PS: I admit, this is a case of abusing the software.
Hi @lh3, many thanks for developing Miniprot!
I was wondering if Miniprot could also be (ab)used to search for very short sequences/peptides (say, even down to 8AA) in large genomes. I successfully used the provided test data trimming the protein down to just MADTQYILP with
-n 1 -l 4 -k 4. Now the weird thing is that I can't find any control peptides (fragments of Myosin or Helicases up to lengths 100) when searching against a full genome (refseq grch38 p14 in this case). Is this expected? Would adjusting parameters help and if yes, which in addition to the above?Many thanks, Andreas
PS: I admit, this is a case of abusing the software.