> Also I don't know *precisely* what the code does. I only know > *vaguely* that > > - it can fragment the query sequence and also the database, and > > - it recomputes the final P and E values based on the set of P and E > values obtained for the query-sequence / database fragments, and > Paracel is proud on the fact that their final P and E values are > identical (plus/minus epsilon) to the P and E values that would have > been obtained by running NCBI Blast on the non-fragmented > query-sequence and the non-fragmented database. I'm convinced it should be possible to get the results exactly the same, although you might have to patch the blast executable a bit.