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 too http://biojava.org/wiki/BioJava:CookBook3:NCBIQBlastService
Perhaps you could send your searches in 25-jobs-at-one-time batches to EMBL's NCBI BLAST REST-based service. At a 25:1 ratio, a set of jobs that take a day would take a little less than an hour (all other things being equal).
As suggested by Josh Herr, you can use blast on your computer to perform large numbers of blasts faster.
The easiest, from my perspective, way to do that would be to have Linux (or MacOSX) installed on a computer, install blast and desired databases and launch the blasts.
If you have no experience with UNIX-like systems, then you would probably need help from a person that is knowledgeable about this.
If you tell us a bit more about your experience, the computer you use or could use in the lab (installed systems, number of CPUs), we may be able to help you some more.
This thread has been there for a long time, but I would like to add a new tip for those who run ncbi-blast+ in their on computers: that if you place the database in a fast storage device (e.g., SSD), you will get a *dramatic* gain in speed!