Question: How to use Repbase with RepeatMasker?

gmei at my-deja.com gmei at my-deja.com
Wed Jun 2 12:34:07 EST 1999


Hi:

I have a question of using Repbase with RepeatMasker.

We have received a licensed version of hrap/cross_match/swat package
and I installed it on our Digital alpha unix machine.

I run "make" file and got the executable of the "cross_match".

I have test run the "RepeatMasker" on the same machine and it worked
fine (I compared the output from our "RepeatMasker" and from
http://www.mgu.har.mrc.ac.uk/repeat/RepeatMasker and they yeilded the
same result). It seems that "RepeatMasker" use the files in "Libraries"
subdirectory to do its comparision.

Now we have also licensed the "Repbase" and got the following files:

README.html  humrep.ref   invrep.ref   plnapp.ref   pseudo.ref
simple.ref
README.txt   humsub.ref   mamapp.ref   plnrep.ref   rodapp.ref
vrtrep.ref
humapp.ref   invapp.ref   mamrep.ref   pseapp.ref   rodrep.ref

So my question is:

In order to use Repbase with RepeatMasker, is it just simply to move
the "ref" files into
the "Libraries" subdirectory of the RepeatMasker? Or I need to do
something else such as to modify RepeatMasker's perl code?

If you reply, please send a copy to  zlmei at hotmail.com

Thanks in advance.

Guang Mei


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