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