[maker-devel] Filtering of ab initio gene models

[Daniel Standage]

Thanks everyone for your responses recently!

The reason for my recent flurry of email activity is that I'm seeing some
unexpected trends when running the new version of Maker with precomputed
alignments. Compared with an annotation I did a while ago (Maker 2.10,
Maker-computed alignments), this new annotation has a substantial number of
new genes annotated. If I compare distributions of AED scores between the
old and new annotation, it's clear that the new annotation has a lot more
low-quality models. If I look at new gene models that do not overlap with
any gene model from the old annotation, the likelihood that it's a
low-quality model is much higher.

I decided to run a little experiment. I annotated a scaffold first using
Maker 2.10 and then using Maker 2.31.3. I both cases, I used the same
pre-computed transcript and protein alignments and the same (latest)
version of SNAP as the only *ab initio* predictor. Maker 2.10 predicted 44
genes while Maker 2.31.3 predicted 63. If we group gene models into loci by
overlap, there are 33 loci with gene models from both 2.10 and 2.31.3, 1
locus with only models from 2.10, and 28 loci with only models from 2.31.3.

Before this experiment, I assumed the issue was related to providing
pre-computed alignments in GFF3 format and perhaps violating some important
assumption. However, this experiment makes me wonder whether there have
been changes to how Maker filters *ab initio* gene models between version
2.10 and version 2.31.3? Do you have any ideas? If it would help, I could
put together a small data set that reproduces the behavior I just described.

Thanks!

--
Daniel S. Standage
Ph.D. Candidate
Computational Genome Science Laboratory
Indiana University
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