<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>snap_masked-$seqid-processed-gene was produced by SNAP on the repeat masked sequence without hints (i.e. the ab initio call).</div><div>maker-$seqid-snap-gene was produced by SNAP after receiving hints from MAKER.</div><div><br></div><div>In both cases MAKER is allowed to add UTR to the model (hence the 'processed' tag).</div><div><br></div><div>--Carson</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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, June 6, 2014 at 10:33 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, Volker Brendel <<a href="mailto:vbrendel@indiana.edu">vbrendel@indiana.edu</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Filtering of ab initio gene models<br></div><div><br></div><div dir="ltr"><div><div>Another question: is there documentation anywhere for the naming conventions of the genes annotated by Maker? Of course it's easy to spot genes based on a particular <i>ab initio</i> gene predictor, as the names are in the IDs. But what is the significance of, say, "snap_masked-$seqid-processed-gene" in a gene ID vs "maker-$seqid-snap-gene"?<br><br></div>Thanks,<br></div>Daniel<br></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Computational Genome Science Laboratory<br>Indiana University<br></div></div><br><br><div class="gmail_quote">On Thu, Jun 5, 2014 at 2:05 PM, Daniel Standage <span dir="ltr"><<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>I have attached data for a small 18kb region with a handful of genes, as well as the corresponding maker_opts.ctl file. (This is a smaller and different data set than what I was looking at yesterday, with a more well-defined problem).<br><br>With the data files as is, Maker 2.31.3 reports a model from 4125 to 6400 with an AED of 0.23. If you exclude transcript TSA024184, Maker reports a different gene from 6111 to 8345 with an AED of 0.01. Both of these genes have transcript support: will Maker report overlapping genes under any conditions? And even if Maker is forced to choose only a single gene to report, why would the model from 4125 to 6400 ever be reported in place of the one from 6111 to 8345, especially since this is provided in the model_gff file?<br><br></div>Even when transcript TSA024184 is included, Maker 2.10 reports the high-confidence gene from 611 to 8345.<br><br></div>Any light you could shed would be helpful. Thanks!<br></div><div class="gmail_extra"><div class=""><br clear="all"><div><div dir="ltr"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Computational Genome Science Laboratory<br>Indiana University<br></div></div><br><br></div><div><div class="h5"><div class="gmail_quote">On Wed, Jun 4, 2014 at 3:17 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>Just eAED, but eAED can affects selection of ab initio results. For example reading frame match of protein evidence which also affects whether evidence from single_exon=1 and genes with single_exon protein evidence get kept. There is also the assumption that your alignments in GFF3 are are correctly spliced (like BLAT does). So giving blastn results as precomputed est_gff would create a lot of noise, since maker ignores blastn and is using it only to seed the polished exonerate alignments.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span><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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, June 4, 2014 at 1:11 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Filtering of ab initio gene models<br></div><div><div><div><br></div><div dir="ltr">I do not provide Gap or Target attributes in the GFF3. Will this affect the AED as well, or just the eAED?<br></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br>Daniel S. Standage<br>
Ph.D. Candidate<br>Computational Genome Science Laboratory<br>Indiana University<br></div></div><br><br><div class="gmail_quote">On Wed, Jun 4, 2014 at 3:09 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>Sure. that would be helpful. One question. Do you provide the Gap attribute in your precomputed alignments? Having or not having that attribute affects the eAED score which takes reading frame into account, and may cause some things to be kept that normally would be dropped, because MAKER won't be able to take the points of mismatch of the alignment into account (it just assumes match everywhere).</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span><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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, June 4, 2014 at 1:03 PM<br><span style="font-weight:bold">To: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Filtering of ab initio gene models<br></div><div><div><div><br></div><div dir="ltr"><div><div><div>Thanks everyone for your responses recently!<br><br></div>The reason for my recent flurry of email activity is that I'm seeing some unexpected trends when running the new version of Maker with precomputed alignments. Compared with an annotation I did a while ago (Maker 2.10, Maker-computed alignments), this new annotation has a substantial number of new genes annotated. If I compare distributions of AED scores between the old and new annotation, it's clear that the new annotation has a lot more low-quality models. If I look at new gene models that do not overlap with any gene model from the old annotation, the likelihood that it's a low-quality model is much higher.<br><br></div>I decided to run a little experiment. I annotated a scaffold first using Maker 2.10 and then using Maker 2.31.3. I both cases, I used the same pre-computed transcript and protein alignments and the same (latest) version of SNAP as the only <i>ab initio</i> predictor. Maker 2.10 predicted 44 genes while Maker 2.31.3 predicted 63. If we group gene models into loci by overlap, there are 33 loci with gene models from both 2.10 and 2.31.3, 1 locus with only models from 2.10, and 28 loci with only models from 2.31.3.<br><br></div>Before this experiment, I assumed the issue was related to providing pre-computed alignments in GFF3 format and perhaps violating some important assumption. However, this experiment makes me wonder whether there have been changes to how Maker filters <i>ab initio</i> gene models between version 2.10 and version 2.31.3? Do you have any ideas? If it would help, I could put together a small data set that reproduces the behavior I just described.<br><br>Thanks!<br clear="all"><div><div><div><div><div><div dir="ltr"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Computational Genome Science Laboratory<br>Indiana University<br></div></div></div></div></div></div></div></div></div>
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