BLAST (Basic Local Alignment Search Tool) is probably the best-known program in sequence analysis. It compares two sequences by trying to align them, and is also used to lookup sequences in a database. The algorithm starts by looking for exact matches, then expands the aligned regions by allowing for mismatches. For details, see Section 7.1 at the end of this chapter.
This chapter contains a guide to the command-line options used in BLAST programs. The programs are listed in the order you might expect to use them. Each entry includes a brief program description, a command-line entry example, and a table summarizing any available options. We're using Version 2.2.5 of BLAST.