[maker-devel] maker and repeatproteinmask

[Mr Thomas Schumann]

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

[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

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[Mr Thomas Schumann]

Ok thanks. I looked through all the RepeatMasker source files and it doesn't look like anything calls RepeatProteinMask, and RepeatProteinMask is the only program which calls trf, so it looks like MAKER doesn't depend on trf at all then.

Thanks,

Tom Schumann

---

From: Carson Holt [cars...@gmail.com]
Sent: Wednesday, 18 July 2012 7:05 AM
To: Mr Thomas Schumann; maker...@yandell-lab.org
Cc: c.ch...@uq.edu.au
Subject: Re: [maker-devel] maker and repeatproteinmask