At compile time, meme-suite checks if its database folder folder exists:

/var/lib/meme-suite

If you have installed any of the meme-db-* packages, this folder will be
present. If you, however, want to install meme-suite first and later set
the databases you need, just make sure that the folder is present before
building meme-suite:

mkdir -p /var/lib/meme-suite

If you want to install the databases manually, they can be downloaded
from here:

http://meme-suite.org/doc/download.html