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

[vdar at yorku.ca]

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
>
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
>