Question about Maker unmask option

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Question about Maker unmask option

Praveen Kumar Raj Kumar
Hi Carson,
      I have a question regarding the following option
unmask=0 #Also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no

Does this mean it is default for MAKER to run ab-initio prediction programs on only masked sequence? If am right masked regions are repeat regions where genes are not present.

And that I feel there should be option to not mask the simple repeats as genes might have those.

Please let me of this. Sorry if I am wrong.

Thank you,
--
Praveen

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Re: Question about Maker unmask option

Carson Hinton Holt
Re: Question about Maker unmask option Simple repeats are soft masked (lower case), so they are still visible to the gene predictor.  It is the high complexity repeats that are hard masked (‘NNNNN’) as they can cause havoc with gene predictors (they ususally encode real proteins, retrotransposase etc.).

Soft masking the simple repeats has the benefic of not seeding alignments in those regions while allowing alignments to extent through them.  This avoids spurious BLAST alignments, and it leaves the sequence available for gene prediction

So setting unmask to 1 basically makes retrotransposon regions visible to the gene predictor.  Not really a good idea, but can sometimes be useful in situations where you believe that transoposons might have been integrated into the real gene structure (rare).

Thanks,
Carson



On 11/22/10 12:20 PM, "Praveen Kumar Raj Kumar" <rpraveenkumardcb@...> wrote:

Hi Carson,
      I have a question regarding the following option
unmask=0 #Also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no

Does this mean it is default for MAKER to run ab-initio prediction programs on only masked sequence? If am right masked regions are repeat regions where genes are not present.

And that I feel there should be option to not mask the simple repeats as genes might have those.

Please let me of this. Sorry if I am wrong.

Thank you,

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maker-devel mailing list
[hidden email]
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