<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="">Use the merged gff3 to train snap, otherwise you won’t have enough models.<div class=""><br class=""></div><div class="">Info on training can be found on the wiki —> <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="">Also you can find additional detailed info by searching the mailing list archives —> <a href="http://groups.google.com/group/maker-devel" class="">http://groups.google.com/group/maker-devel</a></div><div class=""><br class=""></div><div class="">I’m not sure what you are asking with the last question. Alignment is not a function of training, and will not be affected by the hmm, but 100% coverage and identity is too strict a threshold even for data derived from the same species.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 3, 2017, at 9:29 AM, <a href="mailto:dcg@cau.edu.cn" class="">dcg@cau.edu.cn</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="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;" class=""><span class=""></span>Dear sir:</div><div style="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;" class=""> I‘ve been using maker to do my genome annotation. However, I still have something I can't understand:</div><div style="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;" class=""><br class=""></div><div style="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;" class=""> 1. After assembly, I have many contigs. Firstly, I set est2genome=1 and protein2genome=1 , with my proteins, ESTs and RNA-seq..<span class="Apple-converted-space"> </span><b class="">Which way below is correct?</b></div><div style="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;" class=""> 1.1 Each contig has its own gff. I just use its own maker_gff file to get a pyu.hmm(be used in snap practice), and then, train the single contig.</div><div style="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;" class=""> 1.2 I merge all the maker_gff to produce a pyu.hmm(for snap) , and then, use this pyu.hmm to train all the contigs.</div><div style="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;" class=""> </div><div style="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;" class=""> 2. The aim of my project is to find new protein, so I need to guarantee the rigor of my annotation.</div><div style="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;" class=""> <span class="Apple-converted-space"> </span><b class="">I made a plan that the predicted protein should be successfully aligned to the Uniprot(reviewed protein, total number is about 30K) with 100% identity and coverage.</b></div><div style="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;" class=""> However, if I choose method 1.2 as above:</div><div style="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;" class=""> After the first step (est2genome=1 and protein2genome=1), about 1600 proteins can be 100% aligned to the Uniprot. After 2 rounds training(est2genome=0 and protein2genome=0), less proteins can be 100% aligned.</div><div style="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;" class=""> <span class="Apple-converted-space"> </span><b class="">Is my test method reasonable? Why the final results can't get more well aligned proteins?</b></div><div style="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;" class=""><b class=""> </b><b style="font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">After training and fasta_merge, the results can be </b><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">index_all.log.all.maker.proteins.fasta, </span><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">index_all.log.all.maker.snap_masked.proteins.fasta, </span><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class="">index_all.log.all.maker.non_overlapping_ab_initio.proteins.fasta, which is the final results?</span></div><div style="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;" class=""><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""><br class=""></span></div><div style="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;" class=""><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> </span></div><div style="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;" class=""><span style="font-family: ''; font-size: 10.5pt; line-height: 1.5; background-color: window;" class=""> I'm looking forward to hearing from you. Thanks!</span></div><div style="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;" class="">Yours sincerely!</div><div style="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;" class=""><br class=""></div><div style="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;" class=""> </div><div style="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;" class="">Chao Chao</div><hr size="1" align="left" style="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; width: 210px; height: 1px;" class=""><div style="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;" class=""><span class=""><div style="margin: 10px; font-family: verdana; font-size: 10pt;" class=""><div class=""><a href="mailto:dcg@cau.edu.cn" class="">dcg@cau.edu.cn</a></div></div></span></div><span style="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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="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;" class=""><span style="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; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="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;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="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;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: 'Microsoft YaHei UI'; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></body></html>