[maker-devel] Filtering of ab initio gene models

[Carson Holt]

Sure.  that would be helpful.  One question. Do you provide the Gap
attribute in your precomputed alignments?  Having or not having that
attribute affects the eAED score which takes reading frame into account, and
may cause some things to be kept that normally would be dropped, because
MAKER won't be able to take the points of mismatch of the alignment into
account (it just assumes match everywhere).

--Carson


From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Wednesday, June 4, 2014 at 1:03 PM
To:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Filtering of ab initio gene models

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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