I haven't done this myself, but from a quick search on the BioPerl website,
it looks like you'll want to use the
Bio::Tools::Run::RepeatMasker<
http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Tools/Run/RepeatMasker.html>module
to create a repeat-masked fasta file.
If you RepeatMask your query sequence(s), then you need to specify that
sequence when you create your Bio::Seq object.
If you instead RepeatMask your database, you'll need to create a blast
database from the repeat-masked sequences and specify that db in your
@params. I don't think there's a module for running formatdb, but you can do
it through a system call.
Dave
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