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when we did our alignment we got a score of 44 this is the raw score and this score is only dependent on the alignment of the query and the database sequences you know it doesnamp;#39;t depend on anything else it doesnamp;#39;t depend on any other sequences in the database it doesnamp;#39;t depend on the day of the week it doesnamp;#39;t depend on any other calculation and as you might imagine doing that calculation because we have to do the seed where weamp;#39;re finding the exact matches then we have to do the extension where weamp;#39;re keeping track of one of those numbers doing that calculation is computationally quite expensive but this algorithm lends itself beautifully to parallelization because this raw score only depends on two things the two sequences so you can paralyze this application as much as you want you can split the databases up you can split the queries up and as long as you compare everything to everything else and get a list of the raw scores then youamp
