I use the BRIG (BLAST Ring Image Generator) program to compare prokaryote genomes. It executes a local BLAST+ and visualizes the results as rings around the reference genome. I downloaded three genomes (~5 million to ~5.5 million base pairs long) from the NCBI to test the application with. It only took 5 to 10 minutes for BRIG to finish. In my personal experience, BLAST is never that fast. Certainly not while comparing entire genomes. I'm also quite sure my computer is not thát fast and changing BLAST parameters doesn't do much difference. The output appears to be good however.

Is my input just small, is my PC better than I know or is it something I'm not aware of?

What would be a typical time for a run of that magnitude?

Website BRIG
Genomes used:

  • Accession: BA000007.2 GI: 47118301
  • Accession: AE006468.2 GI: 973795115
  • Accession: AL513382.1 GI: 30407157
  • $\begingroup$ If the output looks correct and there are no errors then it could be perfectly fine. The web versions can take a lot longer because the servers are receiving so many queries. $\endgroup$ – James May 19 '16 at 10:41
  • $\begingroup$ @James That makes sense. I just got this weird feeling that something, somewhere is not right. This speed doesn't correspond with my own experience at all. I'm used to BLAST runs that take hours and even days while using grid computing. With this input I expected a run-time of at least a couple of hours because I don't have my grid anymore $\endgroup$ – Iarwain May 20 '16 at 11:49

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