<html><head></head><body 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>On default settings MAKER will only put ab initio predictions that have some sort of evidence support (EST or protein) in the final gene set. The rejected predictions are still in the GFF3 for reference purposes as match/match_part features, but not as gene/mRNA/exon/CDS features. So a lack of evidence might be why it is not there. You can add all rejected models that don't overlap an accepted model by setting keep_preds=1 (this usually brings a lot more into the final gene set than you really want though (lots of false positives). But for some organisms like fungi, which have high gene densities, this approach is relatively safe.</div><div><br></div><div>Alternatively the gene is missing because it overlaps another gene model that was accepted. MAKER won't allow overlapping models on the same strand in eukaryotes. The only way to force that kind of overlap is to give MAKER the reference models in model_gff and not let it call it's own models (then maker is really just aligning evidence and scoring the reference models).</div><div><br></div><div>One final note. If there is no evidence supporting the model, and that is why it is rejected, you can also try adding more evidence to the maker run or you can consider the possibility that the gene model in the reference is not real to being with (i.e. a false positive gene model called during the initial annotation process and not supported by protein or expression data from any source).</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><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> Hung-Wei Hsu <<a href="mailto:ares711122@gmail.com">ares711122@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, 20 May, 2013 12:16 AM<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] Why are some complete gene predictions not present in the final results?<br></div><div><br></div><div dir="ltr">Hi MAKER developers,<div><br></div><div style="">I was exploiting MAKER to perform gene prediction and annotation on my contigs.</div><div style="">I used Artemis to examine gff and found some CDS with complete structure were absent in the final results.</div><div style="">They are really predicted and annotated on the ref genome.</div><div style="">I'm wondering if they were discarded due to overlapping with another CDS.</div><div style="">How can I preserve these CDS?</div><div style="">
Thanks a lot in advance.</div><div style=""><br></div><div style="">Hung-Wei</div></div>
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