Appendix C. NCBI-BLAST Scoring Schemes
parameters for gapped alignment are determined empirically from
random sequence alignments. NCBI-BLAST provides several combinations
of scoring matrices and gap costs. These are the only combinations of
gap penalties that can be used with a given matrix. The default
values for each matrix are in boldface in the following table. If
your BLAST distribution doesn't have all the listed
matrices, you can find more at ftp://ftp.ncbi.nih.gov/blast/matrices.