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
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).
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!