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Hi Quanwei,
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<div class="">MAKER will run Augustus, SNAP, genemark or Fgenesh internally. You can also provide predictions from other gene predictors in valid GFF3 format in the “pred_gff" field in the maker_opts control file. Genemark is self training on your genome. You
provide a path to the “es.mod” file that Genemark makes in the “gmhmm” field. For augustus, the training is more involved, but is described here: <a href="http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.html" class="">http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.html</a></div>
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<div class="">Augustus, snap, Fgenesh, and genemark are all complementary in some respects, but Augustus usually provides the most predictions that MAKER ends up selecting to promote to models. </div>
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<div class="">Hope that helps, </div>
<div class="">Daniel</div>
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<div class="">Daniel Ence<br class="">
Graduate Student<br class="">
Eccles Institute of Human Genetics<br class="">
University of Utah<br class="">
15 North 2030 East, Room 2100<br class="">
Salt Lake City, UT 84112-5330 </div>
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<div class="">On Feb 8, 2017, at 10:45 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div>
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<div class="">Hello:<br class="">
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I am trying to annotate the new genome of a rodent species. I saw a clear pipeline to train the SNAP gene finder. But not clear what I should do if I also want to include augustus and/or GeneMark. Do I need to (could I and how) train it in Maker? In one of
recently published paper, they mention the augustus was trained in Maker, but I am not clear how to do it? I wonder what's you opinions on using other gene finders in Maker. Thanks<br class="">
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<span style="font-size:12pt;font-family:cambria" class="">"Unique features of a global human ectoparasite identified through sequencing of the bed bug genome." Nat Commun, 2016.<u class="">
</u>In this paper, the training step was described as below.<u class=""><br class="">
</u></span>
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<div class=""><b class=""><span style="font-size:12pt;font-family:helvetica" class="">Three rounds of training of the Augustus and SNAP gene predictors within Maker were used to bootstrap to a high-quality training set.</span></b>
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<div class="">Best<br class="">
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<div class="">Quanwei<span style="font-size:12pt;font-family:cambria" class=""></span>
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