<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>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><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><style type="text/css" style="display:none"><!-- p { margin-top: 0px; margin-bottom: 0px; }--></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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