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?
- Accession: BA000007.2 GI: 47118301
- Accession: AE006468.2 GI: 973795115
- Accession: AL513382.1 GI: 30407157