[maker-devel] Poor Exonerate gene model

[Shaun Jackman]

Hi, Carson. I have a case where MAKER is choosing a poor gene model when a
better model exists. The two genes, psaA and psaB, are adjacent and are
similar (37% exonerate score). BLASTX finds only the correct alignments of
psaA and psaB. When exonerate is run, it also finds poor alignments of psaA
to psaB and psaB to psaA. The result is that MAKER chooses the correct
model for psaB, but picks the poor psaB model for psaA. Increasing
ep_score_limit from 20 to 40 works around the issue. I think MAKER could
make a better choice in this situation without that hint. See the attached
screen shots. The first is ep_score_limit=20 and the second
ep_score_limit=40. I’ve attached the evidence GFF.

Cheers,
Shaun

[image: Inline images 1]

[image: Inline images 3]
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