Appendix A. NCBI Display Formats

NCBI-BLAST has several options for displaying sequence alignments. These options are available for the five basic BLAST programs (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX), PSI-BLAST, PHI-BLAST, and MegaBLAST. For all programs, these formats are selected by using the -m option; however, in MegaBLAST, the formats must first be set with the -D 2 option to use classic BLAST formatting. The next section gives a brief description of each option, followed by a detailed explanation and an example.