Does the order of sequences in a blast database matter?

Question

[jon.brate]

I noticed that blasting on the NCBI web site takes longer time if the gene has no matches than if it has a lot. So I was thinking that if the search quickly meets the threshold for number of hits, will it then stop searching? And will the order of the sequences in the database determine which hits gets reported first?

Answer 1

[biotech]

I would say NO, since all possible hits have to been compared before giving the best one, you can try via command line and benchmark.