This search directly compares the input protein queries against a protein database. It is useful in finding other proteins that share sequence similarities to the input query. The matching sequences found by blastp can help determine the function of the input query. A simple example command line is given below.
blastall -p blastp -i my_query -d refseq_protein -F F -o my_output
The above command line searches the input protein query in my_query file against the refseq_protein database. It attempts to identify the exact matches so the filter function was set to false using -F F. The result is saved in my_output.