[Bioperl-l] automated stand alone blast with repeat masker

vdar at yorku.ca vdar at yorku.ca
Tue May 13 16:45:13 EDT 2008

Do we have to install it separately because seems like its not there on my
system although I have bioperl installed on my system.

Quoting Dave Messina <David.Messina at sbc.su.se>:

> I haven't done this myself, but from a quick search on the BioPerl website,
> it looks like you'll want to use the
> 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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