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?
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.