I don't know the details of your algorithm and apologies for assuming ignorance on your part, but did you keep in mind the mantra of databases? It goes something like this (imagine Steve Ballmer saying this): Indexes! Indexes! Indexes!
The code is open available at https://fisheye.tooleserver.org/browse/golem. The short answer is definitely YES. Even with MEMORY engine with no indecies it will be too slow. Indecies just were they are really needed in order to reduce memory consumptions.
mashiah