Question: blastn -no_greedy switch
0
gravatar for pld
5.8 years ago by
pld4.8k
United States
pld4.8k wrote:

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?

ADD COMMENTlink modified 5.8 years ago by Asaf7.0k • written 5.8 years ago by pld4.8k
0
gravatar for Asaf
5.8 years ago by
Asaf7.0k
Israel
Asaf7.0k wrote:

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.

ADD COMMENTlink written 5.8 years ago by Asaf7.0k

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.

ADD REPLYlink written 5.8 years ago by pld4.8k

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

ADD REPLYlink modified 7 weeks ago by RamRS25k • written 5.8 years ago by Asaf7.0k

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.

ADD REPLYlink written 5.8 years ago by pld4.8k
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