<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Upgrade to 2.31.5.</div><div><br></div><div>Changes since 2.31.3</div><div>*a protein2genome issue that was introduced in 2.31.3 was fixed</div><div>*fasta_merge failing with trnascan results issue was fixed</div><div>*other_gff input resulting in ARRAY reference being printed was fixed.</div><div>*naming of tRNA genes was improved to include amino acid identity</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><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> Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu">ranjani@uga.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, May 15, 2014 at 1:00 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, Carson Holt <<a href="mailto:carson.holt@genetics.utah.edu">carson.holt@genetics.utah.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> RE: [maker-devel] FW: protein2genome gene models<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><style type="text/css" style="display:none"><!--P{margin-top:0;margin-bottom:0;} .ms-cui-menu {background-color:#ffffff;border:1px rgb(171, 171, 171) solid;font-family:'Segoe UI WPC','Segoe UI',Tahoma,'Microsoft Sans Serif',Verdana,sans-serif;font-size:10pt;color:rgb(51, 51, 51);} .ms-cui-menusection-title {display:none;} .ms-cui-ctl {vertical-align:text-top;text-decoration:none;color:rgb(51, 51, 51);} .ms-cui-ctl-on {background-color:rgb(223, 237, 250);opacity: 0.8;} .ms-cui-img-cont-float {display:inline-block;margin-top:2px} .ms-cui-smenu-inner {padding-top:0px;} .ms-owa-paste-option-icon {margin: 0px 6px 0px 6px;vertical-align:middle!important;padding-bottom: 2px;display:inline-block;} .ms-rtePasteFlyout-option:hover {background-color:rgb(223, 237, 250) !important;opacity:1 !important;} .ms-rtePasteFlyout-option {padding:8px 4px 8px 4px;outline:none;} .ms-cui-menusection {float:left; width:85px;height:24px;overflow:hidden}.wf {speak:none; font-weight:normal; font-variant:normal; text-transform:none; -webkit-font-smoothing:antialiased; vertical-align:middle; display:inline-block;}.wf-family-owa {font-family:'o365Icons'}@font-face { font-family:'o365IconsIE8'; src:url('https://r4.res.outlook.com/owa/prem/16.0.231.14/resources/styles/office365icons.ie8.eot?#iefix') format('embedded-opentype'), url('https://r4.res.outlook.com/owa/prem/16.0.231.14/resources/styles/office365icons.ie8.woff') format('woff'), url('https://r4.res.outlook.com/owa/prem/16.0.231.14/resources/styles/office365icons.ie8.ttf') format('truetype'); font-weight:normal; font-style:normal;}@font-face { font-family:'o365IconsMouse'; src:url('https://r4.res.outlook.com/owa/prem/16.0.231.14/resources/styles/office365icons.mouse.eot?#iefix') format('embedded-opentype'), url('https://r4.res.outlook.com/owa/prem/16.0.231.14/resources/styles/office365icons.mouse.woff') format('woff'), url('https://r4.res.outlook.com/owa/prem/16.0.231.14/resources/styles/office365icons.mouse.ttf') format('truetype'); font-weight:normal; font-style:normal;}.wf-family-owa {font-family:'o365IconsMouse'}.ie8 .wf-family-owa {font-family:'o365IconsIE8'}.ie8 .wf-owa-play-large:before {content:'\e254';}.notIE8 .wf-owa-play-large:before {content:'\e054';}.ie8 .wf-owa-play-large {color:#FFFFFF/*$WFWhiteColor*/;}.notIE8 .wf-owa-play-large {border-color:#FFFFFF/*$WFWhiteColor*/; width:1.4em; height:1.4em; border-width:.1em; border-style:solid; border-radius:.8em; text-align:center; box-sizing:border-box; -moz-box-sizing:border-box; padding:0.1em; color:#FFFFFF/*$WFWhiteColor*/;}.ie8 .wf-size-play-large {width:40px; height:40px; font-size:30px}.notIE8 .wf-size-play-large {width:40px; height:40px; font-size:30px}.notIE8 .wf-owa-triangle-down-small:before {content:'\e052';}.ie8 .wf-owa-triangle-down-small:before { content:'\e052';}.ie8 .wf-owa-triangle-down-small {color:#666666/*$WFGreyColor*/;}.wf-size-x20 {font-size: 20px!important;}
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--></style><div dir="ltr"><div id="OWAFontStyleDivID" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;"><p>Hi Carson,</p><p><br></p><p>I upgraded to the MAKER version 2.31.3 (from MAKER 2.10). I want to predict gene models directly from proteins. I provided proteins from a related organism as input and set protein2genome to 1. However I do not get any gene models predicted.
</p><p>I also tried this by using a transcriptome data set in addition to the protein dataset and set est2genome and protein2genome to 1. I get gene models from the transcripts but not proteins. When I look at the alignment of the proteins on the genome, they seem
to be aligning rather well and I would expect to see a gene model predicted. </p><p>Would you know why this might be?</p><p><br></p><p>Also the number of gene models predicted (directly from the transriptome)in this version is lower than the previous version I was using (MAKER 2.10). I did notice this version is not predicting overlapping gene models, but that is not rule.</p><p><br></p><p>Thanks,</p><p>Ranjani<br></p><div style="color: rgb(40, 40, 40);"><hr tabindex="-1" style="display:inline-block; width:98%"><div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri,sans-serif"><b>From:</b> maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>> on behalf of Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><b>Sent:</b> Wednesday, April 30, 2014 10:55 AM<br><b>To:</b> Carson Holt; <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b> Re: [maker-devel] FW: protein2genome gene models</font><div> </div></div><div><div>Make sure you're using the current version of MAKER. It works on eukaryotes as well.</div><div><br></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; 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>Carson Holt <<a href="mailto:carson.holt@genetics.utah.edu">carson.holt@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span>Wednesday, April 30, 2014 at 8:53 AM<br><span style="font-weight:bold">To: </span>"<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span>[maker-devel] FW: protein2genome gene models<br></div><div><br></div><div><div style="word-wrap:break-word; color:rgb(0,0,0); font-size:14px; font-family:Calibri,sans-serif"><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><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>Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu">ranjani@uga.edu</a>><br><span style="font-weight:bold">Date: </span>Wednesday, April 30, 2014 at 8:45 AM<br><span style="font-weight:bold">To: </span>"<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>" <<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span>protein2genome gene models<br></div><div><br></div><div><style type="text/css" style="">
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</style><div dir="ltr"><div id="OWAFontStyleDivID" style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif"><p>Hi,</p><p><br></p><p>I want to examine the gene models predicted diectly from protein data for my genome.</p><p>MAKER has an option for this in the maker_opts.ctl file: protein2genome =1 , but it says for prokaryotes only.</p><p><br></p><p>Will this not work for eukaryotes? Is it because of introns?</p><p><br></p><p>Thanks,</p><p>Ranjani<br></p></div></div></div></span></div></div>
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