I am trying to find sequence homology between viral sequences and my protein of interest. I have the sequences of their epitopes which varies from 5 to 500 amino acids long. For shorter sequences, it is recommended to use
blastp-short but I am confused until which length it is okay to run
For shorter sequences, what are the parameters needs to be added for effective results?
blastp -task blastp-short -query POI.fasta -db virus.fasta -out output.txt -outfmt 6 -evalue 20000