[maker-devel] why no prediction

[Mark Yandell]

and finally check the splice sites for the EST splice are they valid GT/AG  or AT/AC?


On May 12, 2015, at 4:18 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Also protein evidence will only be considered as support if it is in the same reading frame as the ab initio prediction. Complete mismatch of reading frames usually suggests a repeat like region.
> 
> —Carson
> 
> 
>> On May 12, 2015, at 4:16 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> 
>> The structure of the evidence appears to suggest a spurious prediction randomly overlapped by a spurious EST alignment. You would need at least protein evidence overlap to make it believable.  There is heavy discordance among the gene predictors. Also the fact that the gene would be 90% plus UTR if the EST does in fact represent true expression is a big factor.  More likely it’s a pseudogene or semi repetitive region. Not making this a gene was the right call.
>> 
>> —Carson
>> 
>> 
>> 
>>> On May 12, 2015, at 3:56 PM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
>>> 
>>> Hi guys,
>>> 
>>> I come with a wired case that one region in genome has evidence, but no gene prediction generated. Here are the detail.
>>> 
>>> 
>>> <image.png>
>>> color means:
>>> pink: Augustus
>>> light green: SNAP
>>> dark pink: pred_gff
>>> light yellow: cufflinks
>>> darkest pink: EST alignment
>>> dark yellow: protein alignment
>>> 
>>> In the region marked by red frame, there are predictions from Augustus and pred_gff, also evidences from cufflinks, why there is no gene model generated? I could find the gene model in the "XXXX.all.maker.non_overlapping_ab_initio.transcripts.fasta" file. It is wired because it did have evidence supported. 
>>> 
>>> Could anyone know the reason?
>>> 
>>> Thanks very much!
>>> 
>>> Best,
>>> Wenbo
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>> 
> 
> 
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