performance question

[Tom Keller]

I hope this isn't off topic. I'm using perl for the following:
Parse a list of start and stop positions for a fairly large (217061 
chars) file of DNA sequence data (m/[acgt]+/i - hopefully Not 
alphabetized!). I have about 200 putative genes demarcated with these 
start and stop positions within that sequence that I wish to further 
analyze. From a performance pov, am I better off reading the same 
larger file 200 times or should I read the large file into memory, 
create 200 smaller files, then pass each of these to my next program?

Thanks,
Tom
-- 
Thomas J. Keller, Ph.D.
MMI Research Core Facility
Oregon Health & Science University
3181 SW Sam Jackson Park Rd
Portland, Oregon  97201
TIMTOWTDI