Hi ,

                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.

 Any help will really be appreciated.