[maker-devel] maker and repeatproteinmask

[Carson Holt]

MAKER calls the 'RepeatMasker' script and is thus dependent on anything
RepeatMasker decides to call internally.  MAKER will never call TRF or
RepeatProteinMask directly, but I can't say whether or not RepeatMasker will
always do so as part of it's normal processing.  The only way to know for
sure is to try.  I removed TRF from my installation and RepeatMasker shows
as completing successfully, so I imagine you would probably be fine without
it.

Thanks,
Carson



From:  Mr Thomas Schumann <thomas.schumann at uqconnect.edu.au>
Date:  Tuesday, 17 July, 2012 1:49 AM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Cc:  "c.chan10 at uq.edu.au" <c.chan10 at uq.edu.au>
Subject:  [maker-devel] maker and repeatproteinmask

Hi, 

Does MAKER require the RepeatProteinMask script from the RepeatMasker
package to function?
I've tried running MAKER with default parameters without this script and it
appears to work fine but I'm not sure if different parameters require
RepeatProteinMask.
And if it is required for MAKER, what file is it called from?

Basically I can't use trf (Tandem Repeat Finder) which is needed for the
RepeatProteinMask script and I'd like to know if trf is required for MAKER
and, if it is, whether the absence of trf has any impact on the results.

Thanks,
Tom Schumann
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