<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="">You can also add additional protein file if you want more evidence than that already in the GFF3. It makes re-annotation and adding evidence to an already annotated genome file really easy.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 17, 2015, at 3:26 PM, Marc Tollis <<a href="mailto:mtollis@asu.edu" class="">mtollis@asu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">I answered my own question:<br class=""></div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">No need to re-align proteins again - takes too long.<br class=""></div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">So, I used the gff file from the gff_merge on the log file from the first run (the one with just protein2genome). Then, after generating the .hmm file, I put it in my control file, along with protein2genome=0, removed the protein.fasta, set maker_gff and protein_pass=1. The output now shows that only snap is running, and no blastx and exonerate - a relief because it is much faster!<br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Sun, Mar 15, 2015 at 7:19 AM, Marc Tollis <span dir="ltr" class=""><<a href="mailto:mtollis@asu.edu" target="_blank" class="">mtollis@asu.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">This is a question about process, and to make sure I am doing things right (when time is of the essence, some mistakes can set you back weeks).</div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;"><br class=""></div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">I have run maker on my de novo vertebrate genome, using only the predictive proteome from a congener (well-studied and available on Ensembl), and generated the HMM for the first round of SNAP training. As per the 2014 tutorial, I edited the control file for this step as follows: I added the path to the .hmm file, and set protein2genome to 0. </div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;"><br class=""></div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">When I run maker, I notice that in addition to snap, it is still running blastx and exonerate however. I noticed that this is because I did not remove (or "comment out") the path to the protein.fa in the control file (the output looks markedly different when I do comment out the protein file - and I can't even tell if it's running snap in this instance). </div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;"><br class=""></div><div class="gmail_default" style="font-family: arial, helvetica, sans-serif; font-size: small;">Is it simply using exonerate to place the ab initio predictions on the scaffolds (meaning that having protein2genome=1 is to tell maker to make evidence annotations) ? Did I do this correctly, or should I also remove the protein.fa out of the control file for SNAP training? </div><div class=""><span style="font-family: arial, helvetica, sans-serif;" class=""></span></div><span class="HOEnZb"><font color="#888888" class="">-- <br class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Marc Tollis, Ph.D.</b></font><div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Post-Doctoral Research Associate</b></font></div><div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Arizona State University</b></font></div><div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">LSE 313</b></font></div><div class=""><font face="courier new, monospace" class=""><b style="background-color:rgb(255,255,255)" class=""><font color="#666666" class=""><a href="tel:%28480%29%20965-7456" value="+14809657456" target="_blank" class="">(480) 965-7456</a></font></b><br class=""></font></div><div class=""><a href="mailto:marc.tollis@asu.edu" target="_blank" class=""><font face="courier new, monospace" class="">marc.tollis@asu.edu</font></a></div><div class=""><font face="courier new, monospace" class=""><b class=""><br class=""></b></font></div><div class=""><font face="courier new, monospace" class=""><b class=""><font color="#666666" class="">website:</font> </b><a href="https://sites.google.com/site/tollisresearch/" target="_blank" class="">https://sites.google.com/site/tollisresearch/</a></font></div><div class=""><font face="courier new, monospace" class=""><b class=""><font color="#666666" class="">blog: </font></b><a href="http://anolistollis.wordpress.com/" target="_blank" class="">anolistollis.wordpress.com</a></font></div></div></div></div></div>
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</blockquote></div><br class=""><br clear="all" class=""><br class="">-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Marc Tollis, Ph.D.</b></font><div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Post-Doctoral Research Associate</b></font></div><div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">Arizona State University</b></font></div><div class=""><font face="courier new, monospace" color="#666666" class=""><b style="background-color:rgb(255,255,255)" class="">LSE 313</b></font></div><div class=""><font face="courier new, monospace" class=""><b style="background-color:rgb(255,255,255)" class=""><font color="#666666" class="">(480) 965-7456</font></b><br class=""></font></div><div class=""><a href="mailto:marc.tollis@asu.edu" target="_blank" class=""><font face="courier new, monospace" class="">marc.tollis@asu.edu</font></a></div><div class=""><font face="courier new, monospace" class=""><b class=""><br class=""></b></font></div><div class=""><font face="courier new, monospace" class=""><b class=""><font color="#666666" class="">website:</font> </b><a href="https://sites.google.com/site/tollisresearch/" target="_blank" class="">https://sites.google.com/site/tollisresearch/</a></font></div><div class=""><font face="courier new, monospace" class=""><b class=""><font color="#666666" class="">blog: </font></b><a href="http://anolistollis.wordpress.com/" target="_blank" class="">anolistollis.wordpress.com</a></font></div></div></div></div></div>
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