<div dir="ltr"><div class="markdown-here-wrapper" style><p style="margin:1.2em 0px!important">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 <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;background-color:rgb(248,248,248)">ep_score_limit</code> 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 <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;background-color:rgb(248,248,248)">ep_score_limit=20</code> and the second <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;background-color:rgb(248,248,248)">ep_score_limit=40</code>. I’ve attached the evidence GFF.</p>


<p style="margin:1.2em 0px!important">Cheers,<br>Shaun</p>
<p style="margin:1.2em 0px!important"><img src="cid:ii_146920094e1f9cbb" alt="Inline images 1" style="margin-right: 25px;"></p>
<p style="margin:1.2em 0px!important"><img src="cid:ii_146921605167b981" alt="Inline images 3" style="margin-right: 25px;"></p>
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