BLAST Advanced Options

BLASTN

	-G  Cost to open a gap [Integer]
		default = 5
	-E  Cost to extend a gap [Integer]
		default = 2
	-q  Penalty for a mismatch in the blast portion of run [Integer]
		default = -3
	-r  Reward for a match in the blast portion of run [Integer]
		default = 1
	-e  Expectation value (E) [Real]
		default = 10.0
	-W  Word size, default is 11 for blastn, 3 for other programs.
	-v  Number of one-line descriptions (V) [Integer]
		default = 100
	-b  Number of alignments to show (B) [Integer]
		default = 100

BLASTP, BLASTX, TBLASTN

	-G  Cost to open a gap [Integer]
		default = 11
	-E  Cost to extend a gap [Integer]
		default = 1
	-e  Expectation value (E) [Real]
		default = 10.0
	-W  Word size, default is 11 for blastn, 3 for other programs.
	-v  Number of one-line descriptions (V) [Integer]
		default = 100
	-b  Number of alignments to show (B) [Integer]
		default = 100

Limited values for gap existence and extension are supported for these three programs. Some supported and suggested values are:

	Existence	Extension

	   10		   1
	   10		   2
	   11		   1
	    8		   2
	    9		   2