<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 is restartable. As long as you run each time in the same location, it can reuse existing alignments from the previous run. You also only need to train on ~10MB of the genome depending on gene density. Target size should be 300-400 genes.<div class=""><br class=""></div><div class="">If you follow this GMOD wiki, this is demonstrated (you can also watch video - link as top of page - to see it being done) —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 10, 2017, at 8:50 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hello: <br class=""><br class=""></div>I am annotating a new genome using Maker. I have RNA-seq assembly and protein sequences (from other organisms) in fasta format. Since I need to train gene finders, so I have to run Maker several times. I think the aligning process between the transcript assembly (protein sequences) and the genome assembly may be time consuming. So I wonder whether I can save such alignment in the first run, and then make use of such alignment in the following runs?<br class=""><br class=""></div>Thanks<br class=""><br class=""></div>Best<br class=""></div>Quanwei<br class=""></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>