blastn -no_greedy switch

Question

[pld]

Does setting the -no_greedy switch make blastn behave like Smith-Waterman? The documentation states that the switch allows blast to "use non-greedy dynamic programming extension". It isn't clear to me what the impact of this switch will have. Does anyone know?

Answer 1

[Asaf]

BLAST will never behave like Smith-Waterman. This option is only applicable using megablast (searching for almost identical sequences), if I understood correctly it will skip the dynamic programming that follows the initial word matching and use greedy algorithm to extend the identical word.

[pld]

It seems to run if I set -task blastn. I am not sure I agree, the help for -no_greedy says: Use non-greedy dynamic programming extension.

[Asaf]

Have a look at table C2 here. Maybe it won't have an effect with -task blastn

[pld]

I realize that it is supposed to work with megablast, I was just saying that it seems to run with blastn as well. Also, it isn't completely true that BLAST will never behave like SW, BLASTP has a flag that forces SW alignments. That is sort of what I'm confused about here: I don't think it is causing megablast to behave like SW, but it is changing the way alignments are generated.