I have a locally created database which contains thousands of protein sequences . I want to check the positive substitutions in every sequence with reference to the target protein as random substitutions were made in every sequence. The format specifier i am using is "positive -Number of positive-scoring matches".
The command line used-
Blastp -query -db -outfmt "7 ssequid mismatch positive ppos "
Query is " Whenever i am running BLAST , it generates only 500 hits, which is may be the default, How can i get the output for all the sequences.
I am new to using command line BLAST. Any help will really be appreciated.