[maker-devel] Short Introns

[Carson Holt]

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" <bioinformatics.umd at gmail.com>
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
>
>
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