Set gapopen and gapextend parameters for psiblast command line

Question

[Amita]

Hello! How can I set gapopen and gapextend parameters as Zero values in psiblast command line for proteins?

Answer 1

[abascalfederico]

If you are using blastpgp:

  -G  Cost to open a gap [Integer]
    default = 11
  -E  Cost to extend a gap [Integer]
    default = 1

However, I don't think it will allow you to set them as 0. Blast has some sets of gap penalties + substitution matrices precalculated from simulations (it needs to estimate the lambda and kappa parameters to estimate e-values). On top of that, I guess you are aware that setting gap penalties to 0 will result in alignments that are biologically meaningless.