[maker-devel] Curious pattern in AED distributions

[Carson Holt]

That’s interesting. It could be a handful of internal filters that help with spurious results.

I use a 0.5 sensitivity/specificity to identify shared edges for a jaccardian split on overlapping evidence clusters for example. There are also a couple of places where if the only thing supporting a model is a single exon blastx hit (i.e. no exonerate, ab initio model, or est splice support, but just a chunk od single exon blastx) then maker will use a reading frame aware AED value of 0.5 as a filter (as in it checks if the reading frame matches and not just raw overlap). If that’s the case, the spike near 0.5 may indicate I needed to be a little strickter than my empirical cutoff estimate. Perhaps 0.4 or 0.45 would be the better cuttoff for these spurious blastx induced models.

—Carson


> On Apr 7, 2019, at 7:25 AM, Lior Glick <liorglic at mail.tau.ac.il> wrote:
> 
> Hi MAKER users,
> Lately I've been performing annotations for multiple genomes from the same species.
> When plotting the histogram of AED scores over all genes, I repeatedly see a very specific pattern, that looks something like this:
> <AED_hist.png>
> This pattern is a bit surprising to me, in two aspects:
> 1) Why is there a surge towards 0.5?
> 2) Why is there a sudden drop right after that surge?
> 
> Has anyone else seen this, or is this a specific outcome of my data/configuration?
> Any ideas of what may cause such a distribution?
> 
> While this is not necessarily an indication of a problem or bug, it does seem a bit odd, and  might imply some bias or artifact.
> Would appreciate your comments.
> Thank you!
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