<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Without commenting on the merits of GMAP vs Blastn or Exonerate, you can provide evidence alignments from any source in gff format in the maker control files. I think for GMAP this would mean converting the sam/bam outputs to a gff3 format, but I don’t know those steps of the top of my head. <div class=""><br class=""></div><div class="">~Daniel </div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 24, 2017, at 5:08 AM, Wen Yao <<a href="mailto:venyao@qq.com" class="">venyao@qq.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" class=""><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;">Dear Guys,<o:p class=""></o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;"><o:p class=""> </o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;">I am using Maker to annotate my genome sequence. However, it costs too much time.<o:p class=""></o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;">By default, Maker use Blastn and Exonerate to align EST or assembled transcripts to the genome.<o:p class=""></o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;">I am wondering if I can use GMAP to align the assembled transcripts to the genome and then provide the<o:p class=""></o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;">alignment to Maker. If so, this may save much time, as GMAP is very fast.</p><p class="MsoNormal" style="line-height: 23.8px;"><br class=""></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;">Thanks!<o:p class=""></o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;"><o:p class=""> </o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;">Best regards,<o:p class=""></o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;"><o:p class=""> </o:p></p></div><div style="font-family: "lucida Grande", Verdana, "Microsoft YaHei";" class=""><p class="MsoNormal" style="line-height: 23.8px;">Wen Yao</p></div>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></div></body></html>