<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">MAKER excludes models without evidence support (this is because gene predictors can overcall by as much as a factor of 10, i.e. lots of false positives). So you may be lacking in either protein or transcript evidence (you should alway supply a minimum of 2 related proteomes for any MAKER analysis - transcript evidence by itself is insufficient).<div class=""><br class=""></div><div class="">You can also try and rescue models based on protein domain content using iprscan. Details in this protocol paper —> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/" class="">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""> </div><div class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 30, 2017, at 1:30 PM, Qihua Liang <<a href="mailto:qlian003@ucr.edu" class="">qlian003@ucr.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Maker Development Team,<br class=""><br class="">Hi, I am using Maker for annotation and BUSCO to evaluate the completeness. <br class=""><br class="">For de novo perditions, I am using Augustus, GeneMark, and SNAP, and the annotated proteins have completeness of ~80%, ~50%, ~50% correspondingly. When I cat all de novo annotated proteins of these three tools, the completeness is much higher as ~92%. <br class=""><br class="">But for all.maker.proteins.fasta, the completeness is only ~80%.<br class=""><br class="">1. Does this mean that some proteins annotated by Augustus/GeneMark/SNAP, are not included in the file all.maker.proteins.fasta? Does it because such excluded proteins do not have hits with the EST evidences?<br class=""><br class="">2. To achieve a higher BUSCO completeness, what possible ways can be used? Including more EST evidences from other species?<br class=""><br class=""><br class="">Thank you<br class="">Qihua<br class="">_______________________________________________<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></div></blockquote></div><br class=""></div></div></body></html>