On 2/19/2011 12:50 PM, Ulrik Mikaelsson wrote:
Just a thought; I guess the references to the non-GC-scanned strings are held in GC-scanned memory, right? Are the number of such references also increased linearly?
Well, first of all, the benchmark I posted seems to indicate otherwise. Second of all, I was running this program before on yeast DNA and it was ridiculously fast. Then I tried to do the same thing on human DNA and it became slow as molasses. Roughly speaking, w/o getting into the biology much, I've got one string for each gene. Yeast have about 1/3 as many genes as humans, but the genes are on average about 100 times smaller. Therefore, the difference should be at most a small constant factor and in actuality it's a huge constant factor.
Note: I know I could make the program in question a lot more space efficient, and that's what I ended up doing. It works now. It's just that it was originally written for yeast, where space efficiency is obviously not a concern, and I would have liked to just try a one-off calculation on the human genome without having to rewrite portions of it.
