==> Maker2 & RepeatMasker

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==> Maker2 & RepeatMasker

Dieter Best-2
Hello,

I started to use Maker2.
1) For now I use it without RepeatMasker. While trying to install the
RepeatMasker Libraries from www.girinst.org I found out that
commercial entities need to pay a fee. Is there a free version of
those libraries available somewhere?
2) blast+: One of the new features appears to be repeat masking. Has
anyone tried Maker2 with blast+ and used repeat masking from blast+?

Thanks,

-- Dieter

--
http://www.linkedin.com/in/dieterbest

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Re: ==> Maker2 & RepeatMasker

Carson Hinton Holt
Re: [maker-devel] ==> Maker2 & RepeatMasker You can also use programs like piler or repeat modeler to produce your own library of species specific repeats for use with repeatmasker and just bypass RebBase altogether.  MAKER also has a te_proteins file used with repeatrunner that will identify repeats, so I doubt there would be that many repeats if any that would be found with RepBase that would not be found with these other methods.  RepBase would be beneficial if you plan on doing an in-depth analysis of repeat types, as the repeats contained in RepBase are categorized and curated.  You would have to categorize piler and repeat modeler repeats yourself.

As I understand it, blast+ can mask out certain human specific repeats during a BLAST, but this does not really help with species other than human.  BLAST+ has a low complexity filter for simple repeats as well, but that is common to all flavors of BLAST including classic NCBI BLAST, and RepeatMasker can identify those even without RepBase libraries.  So I don’t think we would see any real benefits for using BLAST+ inside of MAKER for repeatmasking, at least for species other than Human.

Thanks,
Carson


On 6/4/10 12:18 PM, "Dieter Best" <dieterbest@...> wrote:

Hello,

I started to use Maker2.
1) For now I use it without RepeatMasker. While trying to install the
RepeatMasker Libraries from www.girinst.org I found out that
commercial entities need to pay a fee. Is there a free version of
those libraries available somewhere?
2) blast+: One of the new features appears to be repeat masking. Has
anyone tried Maker2 with blast+ and used repeat masking from blast+?

Thanks,

-- Dieter

--
http://www.linkedin.com/in/dieterbest

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