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<![endif]--><!--StartFragment--><span style="font-size: 10.5pt; font-family: 'Times New Roman'; ">maker seems to prefer to select the snap gene mode, but not genemark</span></div><div style="font-family: Calibri, sans-serif; "><span style="font-size: 10.5pt; font-family: 'Times New Roman'; "><br></span></div><blockquote style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 40px; border-top-style: none; border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; padding-top: 0px; padding-right: 0px; padding-bottom: 0px; padding-left: 0px; "><div style="font-family: Calibri, sans-serif; "><span style="font-size: 10.5pt; font-family: 'Times New Roman'; ">Genemark generally scores lower, and has a very large tendancy to overlap transposons (it can't handled masked fragments, so has to be run on the unmasked genome). Looking through the code base, I now see a section where the non-overlapping model is set to always exclude genemark from the non-overlapping consensus set if there are masked gene predictors such as snap or augustus, and to only accept it's models when the evidence supports it. I'd need to filter genemark candidates for transposon overlap before I could lift this limitation.</span></div><div><font class="Apple-style-span" face="Times New Roman"><br></font></div></blockquote><div><font class="Apple-style-span" face="Times New Roman"><br></font></div><div><font class="Apple-style-span" face="Times New Roman"><span style="font-size: 10.5pt; font-family: 'Times New Roman'; ">Fig 1. the snap gene mode of non_overlapping_ab_initio is redundant (overlapping)
with the maker gene annotation.</span><!--EndFragment--></font></div><div><font class="Apple-style-span" face="Times New Roman"><span style="font-size: 10.5pt; font-family: 'Times New Roman'; "><br></span></font></div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div><font class="Apple-style-span" face="Times New Roman"><span style="font-size: 10.5pt; font-family: 'Times New Roman'; ">The non-overlapping is stranded. These are on different strands. This really does happens in eukaryotes, so if the evidence supports it we have to allow it, and if you set keep_preds=1 you can get it just because the gene predictor supports it reguardless of physical evidence support.</span></font></div><div><font class="Apple-style-span" face="Times New Roman"><span style="font-size: 10.5pt; font-family: 'Times New Roman'; "><br></span></font></div></blockquote><div><font class="Apple-style-span" face="Times New Roman"><span style="font-size: 10.5pt; font-family: 'Times New Roman'; "><span style="font-size: 10.5pt; font-family: 'Times New Roman'; "><br></span></span></font></div><div><font class="Apple-style-span" face="Times New Roman"><span style="font-size: 10.5pt; font-family: 'Times New Roman'; "><!--[if gte mso 9]><xml>
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<![endif]--><!--StartFragment--><span style="font-size: 10.5pt; font-family: 'Times New Roman'; ">Fig 2. the snap gene mode of non_overlapping_ab_initio is redundant (overlapping)
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<![endif]--><!--StartFragment--><span style="font-size: 10.5pt; font-family: 'Times New Roman'; ">Fig.4 no evidence support the snap gene mode. augustus and genemark have
similar results but different from snap. But the snap gene was selected as non_overlapping_ab_initio</span><!--EndFragment--></font></div><div><font class="Apple-style-span" face="Times New Roman"><span style="font-size: 10.5pt; font-family: 'Times New Roman'; "><br></span></font></div><blockquote style="margin:0 0 0 40px; border:none; padding:0px;"><div><font class="Apple-style-span" face="Times New Roman"><span style="font-size: 10.5pt; font-family: 'Times New Roman'; ">Try using Apollo rather than IGV, it becomes so much more obvious because apollo separates the strands into separate panels.</span></font></div></blockquote><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; ">Thanks,</div><div style="font-family: Calibri, sans-serif; ">Carson</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><span id="OLK_SRC_BODY_SECTION" style="font-family: Calibri, sans-serif; "><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Áõ»ÛȪ <<a href="mailto:liuhuiquan@nwsuaf.edu.cn">liuhuiquan@nwsuaf.edu.cn</a>><br><span style="font-weight:bold">Date: </span> Thursday, 18 April, 2013 9:37 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> some strange examples of maker annotation<br></div><div><br></div><div><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">Hi Carson,<!--?xml:namespace prefix = "o" ns = "urn:schemas-microsoft-com:office:office" /--><o:p></o:p></font></span></p><span lang="EN-US" style="font-size: 10.5pt; font-family: 'Times New Roman', serif; ">I run maker on my genome with “keep_preds=1” or “keep_preds=0” respectively. When I manually check the results of maker in Integrative Genomics Viewer (IGV), I found most of the genes annotated by maker were good. But I also view some strange examples for the results. I don’t know how to inteprete these. hope you can give me some suggestions. please see the attached file. thank you very much.<br><!-- -->best regards,<br><!-- -->Huiquan<br><!-- --></span></div></span></div></div></span></body></html>