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Hi Karen,
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<div class="">I don’t of a unified tool that predicts lncRNAs from genomic sequence. I found a tool that predicts lncRNAs from RNAseq dataset, which you might be able to use for your project. I’ve never used it, but it might be a starting place. <a href="http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-311" class="">http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-311</a></div>
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<div class="">Here’s also a review that describes several workflows for annotating lncRNAs in insect genomes: <a href="http://www.sciencedirect.com/science/article/pii/S2214574515000061" class="">http://www.sciencedirect.com/science/article/pii/S2214574515000061</a></div>
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<div class="">Hope that helps, </div>
<div class="">Daniel</div>
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<div class="">Daniel Ence</div>
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<div apple-content-edited="true" 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 Jan 15, 2016, at 3:39 PM, hcma <<a href="mailto:hcma@uci.edu" class="">hcma@uci.edu</a>> wrote:</div>
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<div class="">Hi Carlson,<br class="">
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Regarding non-coding RNA predictions, MAKER only predicts tRNAs and rRNAs, but not other RNAs, for example, lncRNAs?<br class="">
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Thanks again.<br class="">
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Best Regards<br class="">
Karen<br class="">
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On 2016-01-15 09:16, Carson Holt wrote:<br class="">
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<blockquote type="cite" class="">Can maker2 be run without inputting any protein sequences?<br class="">
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Yes. But it will not perform as well.<br class="">
<blockquote type="cite" class="">How to turn this off in the control files?<br class="">
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Any option left blank is off.<br class="">
<blockquote type="cite" class="">Also, can i run maker using Augustus and not SNAP? Again, how do i turn SNAP off?<br class="">
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Yes. Leave it blank.<br class="">
<blockquote type="cite" class="">Does maker also predict non-coding genes?<br class="">
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You can run it with tRNAscan or snoscan. Snoscan requires you to have<br class="">
rRNAs from your organism to train with though.<br class="">
—Carson<br class="">
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