Default Ncbi Blast+ V. 2.2.25 Parameters

Question

[Beeth]

Hi:

I'd like to compare my own BLAST tool with NCBI blast+ tool but couldn't find the default parameter of this version. I'd like to know the scoring scheme for match, mismatch, opening gap and extended gap.

I've created a NCBI blast+ output and it prints at the end of the file:

Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5

For the first line assume that for match 1 and for mismatch -2 is used. and for opening gap they used 0 and for extension gap 2.5?

Thanks, Beeth

Answer 1

[Lyco]

Yes, this is correct. There is some explanation on appropriate parameters for blastn searches that can be found here, but nowhere in the documentation the blast+ defaults are spelled out. For protein searches, the situation is much more complicated (but you are interested in DNA-DNA comparisons, right?)

[Beeth]

yes I am only interested in DNA-DNA comparisons (blastn).

Answer 2

[Käpt'N Silico]

This is a valid question. Even though it is not said in the documentation anywhere, your results should be accompanied by the parameters used. So I ususally use the BLAST XML output format and look through the header. Some parameter values are given there. However, I cannot find any frameshift penalty values with blastx. Does anybody know the default values and shouldn't they be printed in there? Results are only valid in the context of the parameters used!

I've created a related question here.