<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Maker's predictions are improved with evidence. These proteins can be from uniprot (I recommend uniprot50) or from a closely related taxa.</div><div><br></div><div>Maker uses comparisons to these proteins in its prediction. There is more detail on this in the paper.<br><br>Sent from my iPhone</div><div><br>On May 28, 2014, at 3:26, Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com">panos.ioannidis@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr"><div>I'm going through the Maker tutorial and saw that among the input files you give it, there's a fasta file with proteins (the <span style="font-family:courier new,monospace">protein=xxx</span> parameter in the <span style="font-family:courier new,monospace">maker_opts.ctl</span> file).<br>
<br>What exactly are these proteins? I thought Maker both predicts genes (i.e. proteins) and also annotates them. Does it only do annotation of already predicted genes/proteins? But then, why is it using gene predictors like Augustus, SNAP, etc?<br>
<br></div>Thanks,<br>Panos<br></div>
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