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

Dave Messina David.Messina at sbc.su.se
Tue May 13 17:24:45 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.
>

Yes.

BioPerl doesn't include all of the many programs it potentially interacts
with. It'd be great if you could get everything in one shebang, but
practically this isn't possible because there are so many bioinformatics
programs, because they are written and maintained by their authors not by
the BioPerl group, and because they are constantly being updated and the
version included in BioPerl would quickly become out of sync.


>From the Bio::Tools::Run::RepeatMasker documentation:

*To use this module, the RepeatMasker program (and probably database) must
be
installed. RepeatMasker is a program that screens DNA sequences for
interspersed
repeats known to exist in mammalian genomes as well as for low
complexity DNA sequences. For more information, on the program and its
usage, please refer to http://www.repeatmasker.org/. *



Dave


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