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 -- http://mail.python.org/mailman/listinfo/python-list