<html><head><base href="x-msg://154/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Berenice,<div><br></div><div>SNAP is a good gene predictor, but for most genomes Augustus can be more accurate - of course it is also harder to train. Running a first round of MAKER annotation with SNAP as the predictor and then training SNAP on the output from that run followed by a second MAKER run (runs pretty fast second time because all the blast jobs are reused) is a good way to start. Ultimately running Augustus as well (along with custom training) is probably worth it for a final annotation effort. The good thing is you can run these iterative cycles of annotation with minimal effort because MAKER will reuse an computations that have already run.</div><div><br></div><div>B</div><div><br><div><div>On Jun 7, 2013, at 3:58 PM, Daniel Ence wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><div><br class="Apple-interchange-newline"><br><div class="BodyFragment"><font size="2"><div class="PlainText">Daniel Ence<br>Graduate Student<br>Eccles Institute of Human Genetics<br>University of Utah<br>15 North 2030 East, Room 2100<br>Salt Lake City, UT 84112-5330</div></font></div></div><div style="font-family: 'Times New Roman'; color: rgb(0, 0, 0); font-size: 16px; "><hr tabindex="-1"><div id="divRpF42143" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b><span class="Apple-converted-space"> </span><a href="mailto:berenice.benayoun@gmail.com">berenice.benayoun@gmail.com</a><span class="Apple-converted-space"> </span>[<a href="mailto:berenice.benayoun@gmail.com">berenice.benayoun@gmail.com</a>] on behalf of Bérénice Benayoun [<a href="mailto:benayoun@stanford.edu">benayoun@stanford.edu</a>]<br><b>Sent:</b><span class="Apple-converted-space"> </span>Friday, June 07, 2013 3:50 PM<br><b>To:</b><span class="Apple-converted-space"> </span>Daniel Ence<br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [maker-devel] Maker and mono-exonic genes ?<br></font><br></div><div></div><div>Hi Daniel,<div><br></div><div>Thanks for the quick answer !</div><div><br></div><div>I used SNAP, and trained from a hmm model made with the CEGMA output on my genome (240 gene models) plus a first run of maker of 1/3 of the genome. I tried GenemarkES and Augustus, but for some reason they don't run, so I stopped indicating their existence to maker.</div><div><br></div><div>Should I do something in particular to train it "better" ? Is there any other predictor that would be worth running ? </div><div><br></div><div>Thanks so much for your help !</div><div><br></div><div>Berenice<br><br><div class="gmail_quote">2013/6/7 Daniel Ence<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>></span><br><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; "><div><div style="direction: ltr; font-size: 10pt; font-family: Tahoma; ">Hi Berenice, Thank you for sending that screenshot and the maker_opts.log file. Those are exactly what we need to understand how to expect MAKER to perform. <div><br>In looking at the screenshot, it doesn't look like any of the gene predictors gave a prediction in this region. Uses the predictions from ab-initio tools as a basis for models and considers models that are supported by evidence. It won't by default create a model when there isn't a prediction in the region. </div><div><br>Can I ask which gene predictors you used and how they were trained? You might consider training one or more of them on the specific evidence that you expect to support these genes and then rerunning maker with the retrained predictors. </div><div><br>Thanks,</div><div>Daniel<br><div><br><div><font><div>Daniel Ence<br>Graduate Student<br>Eccles Institute of Human Genetics<br>University of Utah<br>15 North 2030 East, Room 2100<br>Salt Lake City, UT 84112-5330</div></font></div></div><div style="font-size: 16px; font-family: 'Times New Roman'; "><hr><div style="direction: ltr; "><font face="Tahoma" color="#000000"><b>From:</b><span class="Apple-converted-space"> </span>maker-devel [<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-lab.org</a>] on behalf of Bérénice Benayoun [<a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a>]<br><b>Sent:</b><span class="Apple-converted-space"> </span>Friday, June 07, 2013 11:17 AM<br><b>To:</b><span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>[maker-devel] Maker and mono-exonic genes ?<br></font><br></div><div><div class="h5"><div></div><div>Dear maker developers,<div><br></div><div>I am currently annotating a de novo fish genome, and have started looking for genes of interest in particular in Maker's output to verify that it's outputting proper gene sets.</div><div><br></div><div>While many of the genes I look for seem to be correctly annotated by the pipeline, I have noticed that important genes that do have strong evidentiary support but are monoexonic are NOT reported by maker. </div><div><br></div><div>I am attaching a screenshot for the contig that I know should contain the<span class="Apple-converted-space"> </span><i>Foxl2</i><span class="Apple-converted-space"> </span>gene (notoriously monoexonic across evolution), and highlighted the corresponding evidence for it.</div><div><br></div><div>Is there any setting I can give to maker to force it to output monoexonic genes ? I already set "single_exon=1" with no success. I attached my config file FYI.</div><div><br></div><div>Thank you so much in advance for your answer !!!</div><div><br></div><div>Best,</div><div><br></div><div>Berenice.</div><div>--<span class="Apple-converted-space"> </span><br><font>Bérénice A. BENAYOUN, Ph.D.</font><br>Stanford University/Genetics Department<br><i>BRUNET Laboratory</i>, 'Molecular Basis of Longevity and Age Related Diseases'<br>M312 Alway Building<br>300, Pasteur Drive<br><span>MC 5120<span class="Apple-converted-space"> </span><br>Stanford, CA 94305-5120</span><br>USA<br>Email:<span class="Apple-converted-space"> </span><a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a><br>Web:<span class="Apple-converted-space"> </span><a href="http://www.stanford.edu/group/brunet/" target="_blank">www.stanford.edu/group/brunet/</a><a href="http://www.stanford.edu/group/brunet/" target="_blank"></a></div></div></div></div></div></div></div></div></blockquote></div><br><br clear="all"><div><br></div>--<span class="Apple-converted-space"> </span><br><font>Bérénice A. BENAYOUN, Ph.D.</font><br>Stanford University/Genetics Department<br><i>BRUNET Laboratory</i>, 'Molecular Basis of Longevity and Age Related Diseases'<br>M312 Alway Building<br>300, Pasteur Drive<br><span>MC 5120<span class="Apple-converted-space"> </span><br>Stanford, CA 94305-5120</span><br>USA<br>Email:<span class="Apple-converted-space"> </span><a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a><br>Web:<span class="Apple-converted-space"> </span><a href="http://www.stanford.edu/group/brunet/" target="_blank">www.stanford.edu/group/brunet/</a><a href="http://www.stanford.edu/group/brunet/" target="_blank"></a></div></div></div></div>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></span></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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