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Set gapopen and gapextend parameters for psiblast command line

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

alignment blast
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updated by abascalfederico abascalfederico • written by Amita • Amita

1 answer

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.

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written by abascalfederico abascalfederico

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