<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">For fungi, I've put up some of the gene prediction parameters that I've built or trained if that is a helpful for you.<div><br></div><div><a href="https://github.com/hyphaltip/fungi-gene-prediction-params">https://github.com/hyphaltip/fungi-gene-prediction-params</a></div><div><br></div><div>In the absence of any ESTs or RNA-Seq I also recommend generating a starting training set with CEGMA first and then training your predictors from there except for GeneMark.hmm which seems to do okay with self-training.</div><div><br></div><div>Jason<br><div><div>On Mar 18, 2013, at 10:49 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif; "><div>You didn't supply any evidence or HMM files for gene predictors. Just raw assembly data by itself is insufficient for genome annotation.</div><div><br></div><div>Here is some nice documentation for running MAKER --> <a href="http://gmod.org/wiki/MAKER_Tutorial_2012">http://gmod.org/wiki/MAKER_Tutorial_2012</a></div><div>Here is a nice overview of genome annotation ion general --> <a href="http://fasta.bioch.virginia.edu/cshl/pdf/12/ajm12/euk_genome_annotation_review.pdf">http://fasta.bioch.virginia.edu/cshl/pdf/12/ajm12/euk_genome_annotation_review.pdf</a></div><div><br></div><div>Once you've gone through the documentation and examples, if you come across any questions just let us know.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223); "><span style="font-weight:bold">From: </span> "Borhan, Hossein" <<a href="mailto:Hossein.Borhan@AGR.GC.CA">Hossein.Borhan@AGR.GC.CA</a>><br><span style="font-weight:bold">Date: </span> Monday, 18 March, 2013 4:40 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] failed gene prediction<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; "><div style="font-family: Calibri, sans-serif; ">Hi</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; ">I have tried maker on a fungus genome of 45 mb with 1/3 being repeat rich. It did not produce any prediction. I am not sure what is causing this. Attached are the STDERR and opts.ctl. I appreciate your help</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; ">Hossein</div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div style="font-family: Calibri, sans-serif; "><br></div><div><div style="font-size: 14px; "><br></div><div style="font-family: Calibri, sans-serif; "><div style="font-family: Calibri, sans-serif; font-size: 14px; margin: 0cm 0cm 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px; "><br></span></font></div><div style="font-family: Calibri, sans-serif; font-size: 14px; margin: 0cm 0cm 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></div><div style="font-family: Calibri, sans-serif; font-size: 14px; margin: 0cm 0cm 0.0001pt; "><font class="Apple-style-span" face="Arial,sans-serif"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></div></div></div></div></div>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); 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>Jason Stajich</div><div><a href="mailto:jason.stajich@gmail.com">jason.stajich@gmail.com</a></div><div><a href="mailto:jason@bioperl.org">jason@bioperl.org</a></div></span>
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