<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Carlson, <div><div><div>Thanks for your help!</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>The way you proceed depends on why the genes are not there to begin with. Are they not there because of a lack of evidence? </div></div></blockquote><br>It is a mixture of cases, and I can only look at some examples to say that. There are cases where all 3 used ab initio predictors provide models, there are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus no model is retained. i guess my default parameters could be responsible for these cases at least.</div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>If that's the case just adding the new fasta file should do the trick. </div></div></blockquote><br>which fasta do you refer to? The proteins file I use as evidence contains all proteins i can actually use.</div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Or are they not there because an assembly error makes it impossible to get a logical model for the region (I.e reading frame breaks). </div></div></blockquote><br>This is not the case in general.</div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Are there ab initio models already called in those regions that could just be promoted to the annotation tier? You can test that one by blasting against the nonoverlaping_abinits.fasta files.</div></div></blockquote><br>I have not done this, will do!<br><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div><br></div><div>For any of the cases described, you can provide the existing annotation set as the input in GFF3 format, and previous models will be maintained preferentially. </div></div></blockquote><br>You mean in a new maker run? is this possible with the old maker as well, not maker2, right?</div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence. Attached is a script that would make selecting those easier. It take the MAKER generated GFF3 and a list of predictions to keep (one name per line). These might be the results of a BLAST analysis for example. It will then return the GFF3 entries for just those models selected.</div></div></blockquote><br>The thing is, for the few cases I have looked at, I cannot really decide which model is the best, and the 3 models from the ab initio predictors do not agree on the exact intron-exon junctions or the start and stop codons.<br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div><br></div><div>If the situation is more complex, just provide more detail, and I am sure we can help you come up with a plan.</div><div><br></div></div></blockquote>What i was thinking to do was to provide a gff file of alignments (eg by exonerate) to the proteins of the closely related species that i am missing, and somehow keep the previous annotations and get the extra ones by this gff file. But how exactly maker should be run to do this I am not sure. if I want to keep the previous annotations I need the gff file of the last maker run as input, but then how do I discriminate with the exonerate gff file? And which mode of rediction should be on, and with which parameters? You mention <span class="Apple-style-span" style="font-family: Calibri, sans-serif; font-size: 14px; ">keep_preds=1 for the existing annotations, but how do i also promote evidence from alignments on the same way in the same run?</span></div><div><font class="Apple-style-span" face="Calibri, sans-serif" size="4">Looks feasible though. </font><span class="Apple-style-span" style="font-family: Calibri, sans-serif; ">Thanks again,</span></div><div>Anastasia</div><div><br><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-family: Calibri, sans-serif; "><div>Thanks,</div><div style="font-size: 14px; ">Carson</div><div style="font-size: 14px; "><br></div><span id="OLK_SRC_BODY_SECTION" style="font-size: 14px; "><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Anastasia Gioti <<a href="mailto:anastasia.gioti@scilifelab.se">anastasia.gioti@scilifelab.se</a>><br><span style="font-weight:bold">Date: </span> Wed, 25 Apr 2012 11:09:36 +0200<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Use pass-through system to add missing genes<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi, <div>I have a set of predicted proteins from the genome of a fungus annotated by MAKER using EST data from a closely related species and 3 ab initio predictors (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.</div><div>I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?</div><div>Thanks, </div><div>Anastasia</div><div><br></div><div><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">Anastasia Gioti<br>Post-doctoral Researcher<br><br><a href="mailto:anastasia.gioti@scilifelab.se">anastasia.gioti@scilifelab.se</a><br><a href="mailto:anastasia.gioti@ebc.uu.se">anastasia.gioti@ebc.uu.se</a><br><br><a href="http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/">http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/</a><br><br><br></span></div><br></div></div></div>_______________________________________________
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<span><gff3_select></span></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">Anastasia Gioti<br>Post-doctoral Researcher<br><br><a href="mailto:anastasia.gioti@scilifelab.se">anastasia.gioti@scilifelab.se</a><br>anastasia.gioti@ebc.uu.se<br><br>http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/<br><br><br></span>
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