Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. It only takes a minute to sign up.
Sign up to join this community
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?
blastp -task blastp-short -query POI.fasta -db virus.fasta -out output.txt -outfmt 6 -evalue 20000
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.
word_size and window_size in the parameters?
$\endgroup$
word_size parameter is used in the initial search when BLAST makes a table of all possible "words" present in the query sequence. This first search is not only for identical "words" but for all "words" that would yield an alignment with a score above a threshold, with this step, BLASTp increases speed at the expense of only a small loss in sensitivity by only trying to extend a "hit" if there is a second "hit" within a certain window_size.
$\endgroup$
word_size effects my BLASTp result? If I want to find 5 or 6 amino acid match at least then increasing word_size to 5 or 6 will help? It means it will try to find 5 or 6 amino acids initial match?
$\endgroup$