For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm using NCBIQBlastService to do my alignment remotely and as I checked for each request it would take 20 sec so for the whole 4000 it would take around a day. Is there any other way to do this faster. any suggestion would be really appriciated. and BTW this might help toohttp://biojava.org/wiki/BioJava:CookBook3:NCBIQBlastService
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