BLAST

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Chapter 13

CHAPTER 13

NCBI-BLAST Reference

This chapter describes the parameters and options for the NCBI suite of BLAST pro-

grams. The NCBI distribution includes the blastall program, plus several ancillary

programs that are either necessary for blastall (e.g., formatdb) or provide other

BLAST-like searches that aren’t included within blastall (e.g., blastpgp and

blastclust). This reference also describes the various command-line parameters for

the most important executables.

Usage Statements

If you forget the syntax for a particular parameter, you can view a usage statement

from most programs by typing the program name followed by a dash (in some cases

the dash isn’t required, but it’s easier to remember to use a dash with all programs).

For example:

blastall -

formatdb -

fastacmd -

megablast -

bl2seq -

blastpgp -

blastclust -

Command-Line Syntax

All parameters for NCBI-BLAST programs are single letters and must be preceded by

a single dash. Unlike many common Unix programs, the parameters for NCBI pro-

grams are never concatenated. All parameters may take arguments, including those

that operate as true/false (T/F) switches. For such switches, the T/F is case-insensi-

tive, and the argument may be omitted, in which case the switch is set to T. Finally,

the space between the parameter and ...