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 blastp?
For shorter sequences, what are the parameters needs to be added for effective results?
You should increase the -evalue 10 default option to a higher value because this value it's adjusted to the sequence database size. Check this table, maybe this can help you to decide which parameters are the best option for you.
OPTION TASK DEFAUL DESCRIPTION
word_size blastp 3 Word size of initial match.
word_size blastp-short 2 Word size of initial match.
gapopen blastp 1 Cost to open a gap.
gapopen blastp-short 9 Cost to open a gap.
gapextend blastp 1 Cost to extend a gap.
gapextend blastp-short 1 Cost to extend a gap.
matrix blastp BLOSUM62 Scoring matrix name.
matrix blastp-short PAM30 Scoring matrix name.
threshold blastp 11 Minimum score to add a word to the BLAST lookup table.
threshold blastp-short 16 Minimum score to add a word to the BLAST lookup table.
window_size blastp 40 Multiple hits window size, use 0 to specify 1-hit algorithm.
window_size blastp-short 15 Multiple hits window size, use 0 to specify 1-hit algorithm.