<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><font face="Calibri,sans-serif">That's what I'd do. But really </font><span style="font-size: 15px;">protein2genome=1 is just meant to get enough rough gene models to train a gene predictor. You don't need to run it across the whole genome. But if you do, when you run again after training the gene predictor, MAKER will detect the old BLAST jobs and they won't have to rerun on the second MAKER run.</span></div><div><span style="font-size: 15px;"><br></span></div><div><span style="font-size: 15px;">--Carson</span></div><div><span style="font-size: 15px;"><br></span></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><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, June 5, 2014 at 12:56 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> RE: [maker-devel] protein2genome gene models from protein gff<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/16.0.245.8/resources/styles/office365icons.ie8.eot?#iefix') format('embedded-opentype'), url('https://r4.res.outlook.com/owa/prem/16.0.245.8/resources/styles/office365icons.ie8.woff') format('woff'), url('https://r4.res.outlook.com/owa/prem/16.0.245.8/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/16.0.245.8/resources/styles/office365icons.mouse.eot?#iefix') format('embedded-opentype'), url('https://r4.res.outlook.com/owa/prem/16.0.245.8/resources/styles/office365icons.mouse.woff') format('woff'), url('https://r4.res.outlook.com/owa/prem/16.0.245.8/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>So what would you suggest is the best way to get protein2genome predictions? Use fasta sequences, instead of gff?</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> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><b>Sent:</b> Thursday, June 05, 2014 2:08 PM<br><b>To:</b> Sivaranjani Namasivayam; <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b> Re: [maker-devel] protein2genome gene models from protein gff</font><div> </div></div><div><div>est_gff assumes the alignments are spliced correctly. The protein2genome option also makes that assumption but with a little less confidence that the user always provides splice aware alignments, so in some instances (like protein2genome=1) it may not
pass them forward as guaranteed splice aware alignments.</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>Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu">ranjani@uga.edu</a>><br><span style="font-weight:bold">Date: </span>Thursday, June 5, 2014 at 9:49 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] protein2genome gene models from protein gff<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,<br></p><p><br></p><p>I am trying to predict gene models from protein evidence, using the parameter protein2genome set to 1.<br></p><p><br></p><p>I get gene models predicted if I provide the proteins as a fasta file, but not as gff (I want to use a gff format to avoid the blastx step again). Is this expected?<br></p><p><br></p><p>In case of transcriptome evidence and est2genome set to 1, I get gene models predicted with both fasta and gff formats.<br></p><p><br></p><p>Thanks,<br></p><p>Ranjani<br></p></div></div></div>
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