<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">The est2genome=1 one option in MAKER2 only works with input fasta files because it’s based on Exonerate’s est2genome alignments. It does not with with GFF3 input (gff3 is missing some things that are in the exonerate report). MAKER3 however will let you do this with GFF3 input (it goes back and tries to predict missing info that Exonerate would have produced).<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 2, 2019, at 7:21 PM, <a href="mailto:ychliu@genetics.ac.cn" class="">ychliu@genetics.ac.cn</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class=""></span>Dear MAKER developers,</div><div style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgba(0,="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: "";" class=""> </span><span style="font-family: ""; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> I recently use the MAKER to do gene annotation. But even I use the gff3 file as the EST evidence, the result shows no gene that marked by est2genome (I do use the parameter </span><span style="font-family: ""; font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">est2genome=1</span><span style="background-color: window; font-family: ""; font-size: 10.5pt; line-height: 1.5;" class="">). It may means that the gff3 seems doesn't work. So what's the problem? How can I solve it? Eager for you assistance.</span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgb(255,="" 255,="" 255);="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: "";" class=""> </span><span style="font-family: ""; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> </span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">Faithfully yours.</span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgb(255,="" 255,="" 255);="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: "";" class=""> </span><span style="font-family: ""; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> Yucheng Liu</span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><hr size="1" align="left" style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; width: 210px; height: 1px;" class=""><div style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class=""><b class="">Yucheng Liu</b><div class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgba(0,="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: "";" class="">Institute of Genetics and Developmental Biology, CAS</span></div><div class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgba(0,="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: "";" class="">Beijing, 100101 China</span></div><div class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgba(0,="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: "";" class="">Tel: 86-010-64801362</span></div><div class=""><span microsoft="" yahei="" ui'";="" font-size:="" 14px;="" color:="" rgb(0,="" 0,="" 0);="" background-color:="" rgba(0,="" font-weight:="" normal;="" font-style:="" normal;text-decoration:="" none;'="" style="font-family: "";" class="">E-mail:<span class="Apple-converted-space"> </span><a href="mailto:ychliu@genetics.ac.cn" class="">ychliu@genetics.ac.cn</a></span></div></span></div><span style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: "Microsoft YaHei UI"; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; 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