Estimating memory use?

[Tim N. van der Leeuw]

Hi,

What is your 'static' data (database), and what is your input-data?
Those 200.000 probes are your database? Perhaps they can be stored as
pickled compiled regexes and thus be loaded in pickled form; then you
don't need to keep them all in memory at once -- if you fear that
memory usage will be too big.

I don't know if perhaps other string-matching techniques can be used
btw; you don't need the full power of regexes I guess to match DNA
string patterns.
Perhaps you should investigate that a bit, and do some performance
tests?

cheers,

--Tim