Appendix C. NCBI-BLAST Scoring Schemes

`Statistical 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.