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Old 06-29-2010, 10:49 AM   #3
Location: NJ

Join Date: Feb 2010
Posts: 55

Here's the official response from NCBI. Only some of the code is multithreaded..

"BLAST search has three distinctive stages: word matching with database scan, ungapped alignment, gapped alignment with traceback.

As I understand it Only the word match stage is multi-threaded. So what you described make sense and it correct."
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