Does anyone know of a (UNIX/X) program that will strip ALU (et al.) out of
sequences before they are used for homology searches? We are doing this
crudely now using BLASTs against a local, small ALU database. We'd like
to do this automatically.
Also, is there a publicly-available ALU database out there that we can
use to improve our local database?
Thanks in advance.
bayer at darwin.med.utah.edu