Short Introns

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Short Introns

UMD Bioinformatics
Hello,

We are preparing two submission for NCBI, nightmare. However some of our MAKER gene models have short introns that are being flagged by NCBI. In one species we have >400 introns smaller then 20bp which is almost biologically impossible. I know we can set max intron length in the opts.ctl file but can we set a minimum intron length?

I saw yesterdays posts that mention this is a result of the external ab initio predictors but I didn’t see an indication as to which predictor and how to change that setting.

from yesterday:
*These are just short introns (intron size is under control of the ab initio
predictors) -->   438 ERROR:   SEQ_FEAT.ShortIntron

Cheers
Ian


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Re: Short Introns

Carson Holt-2
Look at the name of those genes.  The original name will let you know
where it came from because it will contain, augustus, genemark, snap, etc.
 You will also want to open up the contig containing those geens in a
viewer like apollo
(http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz).  See if the
short intron is part of the CDS or UTR.  If it's UTR then, it has evidence
support from an EST, which either means there are problems with the
EST/cDNA evidence or it's real.  For those, even if they are real you can
just trim them off.  If it's part of the CDS, then investigate whether it
is suggested by EST or protein evidence, or if the ab initio predictor
called it (sometime the ab initio predictor calls things to force an ORF
to work).  This can sometimes be indicative of assembly issues in that
region.

--Carson


On 4/18/14, 7:14 AM, "UMD Bioinformatics" <[hidden email]>
wrote:

>Hello,
>
>We are preparing two submission for NCBI, nightmare. However some of our
>MAKER gene models have short introns that are being flagged by NCBI. In
>one species we have >400 introns smaller then 20bp which is almost
>biologically impossible. I know we can set max intron length in the
>opts.ctl file but can we set a minimum intron length?
>
>I saw yesterdays posts that mention this is a result of the external ab
>initio predictors but I didn’t see an indication as to which predictor
>and how to change that setting.
>
>from yesterday:
>*These are just short introns (intron size is under control of the ab
>initio
>predictors) -->   438 ERROR:   SEQ_FEAT.ShortIntron
>
>Cheers
>Ian
>
>
>_______________________________________________
>maker-devel mailing list
>[hidden email]
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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Re: Short Introns

Carson Holt-2
I think you may be best off using WebApollo to manually annotated the few
hundred short intron ones.  It's not that fun to do, but you should be
able to get them all in a couple of days by yourself or under a day if you
had a helper.

--Carson


On 5/15/14, 11:15 AM, "Mack, Brian" <[hidden email]> wrote:

>Hi, I examined the genes that had introns less than 10 bp that were being
>flagged by tbl2asn and I noticed that all 438 of them were genes called
>by SNAP. Also they were found in the CDS and not the UTR. It seems
>strange that all of the genes that have these short introns are from SNAP
>when only about one third of the final gene models are from SNAP. I've
>examined the evidence for a handful of these genes and the short introns
>do not seem supported by the evidence. Has anybody else had short intron
>issues with SNAP?
>
>Brian
>
>-----Original Message-----
>From: maker-devel [mailto:[hidden email]] On Behalf
>Of Carson Holt
>Sent: Friday, April 18, 2014 10:36 AM
>To: UMD Bioinformatics; [hidden email]
>Subject: Re: [maker-devel] Short Introns
>
>Look at the name of those genes.  The original name will let you know
>where it came from because it will contain, augustus, genemark, snap, etc.
> You will also want to open up the contig containing those geens in a
>viewer like apollo
>(http://weatherby.genetics.utah.edu/apollo/apollo.tar.gz).  See if the
>short intron is part of the CDS or UTR.  If it's UTR then, it has
>evidence support from an EST, which either means there are problems with
>the EST/cDNA evidence or it's real.  For those, even if they are real you
>can just trim them off.  If it's part of the CDS, then investigate
>whether it is suggested by EST or protein evidence, or if the ab initio
>predictor called it (sometime the ab initio predictor calls things to
>force an ORF to work).  This can sometimes be indicative of assembly
>issues in that region.
>
>--Carson
>
>
>On 4/18/14, 7:14 AM, "UMD Bioinformatics" <[hidden email]>
>wrote:
>
>>Hello,
>>
>>We are preparing two submission for NCBI, nightmare. However some of
>>our MAKER gene models have short introns that are being flagged by
>>NCBI. In one species we have >400 introns smaller then 20bp which is
>>almost biologically impossible. I know we can set max intron length in
>>the opts.ctl file but can we set a minimum intron length?
>>
>>I saw yesterdays posts that mention this is a result of the external ab
>>initio predictors but I didn’t see an indication as to which predictor
>>and how to change that setting.
>>
>>from yesterday:
>>*These are just short introns (intron size is under control of the ab
>>initio
>>predictors) -->   438 ERROR:   SEQ_FEAT.ShortIntron
>>
>>Cheers
>>Ian
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>[hidden email]
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
>_______________________________________________
>maker-devel mailing list
>[hidden email]
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
>
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