<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Carson,</div><div><br></div><div>How hard would it be to have maker take an option something like 'require_abinits=2' that would instruct maker to promote predictions that overlap with (2, 3 or more) other predictions? Seems like the maker might have all that info in one place at some point already?</div><div><br></div><div><div><div>Gowthaman, your contributions to the maker tutorial would be most welcome. I've got an offline copy of a newer tutorial wiki that is more up to date than the GMOD version. It's on a server right now that we've got locked behind a firewall, but I'm hoping to move that to a public facing server in the next week and I'd be happy to give you an account on the wiki.</div></div></div><div><br></div><div>B</div><br><div><div>On May 30, 2012, at 6:54 AM, Carson Holt wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>It's not an option in exactly the way you are specifying, but there is<br>something I usually do for annotation that works well. I run interproscan<br>or rpsblast on the non_overlapping.proteins.fasta file and select just<br>those non-overlapping models that have a recognizable protein domain (just<br>searching the pfam doamin space is more than sufficient). Then I provide<br>the selected results to model_gff, and provide the previous maker results<br>to the maker_gff option with (all reannotation pass options set to 1 and<br>all analysis options turned off). This adds models with at least<br>recognizable domains (as even multiple gene predictors can overpredict in<br>a similar way).<br><br>Attached is a script to help select predictions and upgrade them to models<br>in GFF3 format. If you have question let me know.<br><br>Thanks,<br>Carson<br><br><br><br>On 12-05-29 5:54 PM, "Gowthaman Ramasamy"<br><<a href="mailto:gowthaman.ramasamy@seattlebiomed.org">gowthaman.ramasamy@seattlebiomed.org</a>> wrote:<br><br><blockquote type="cite">Hi Carson,<br></blockquote><blockquote type="cite">Thanks for all the help during the long weekend, in spite of that long<br></blockquote><blockquote type="cite">drive. I am still trying to imagine that.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I now have maker to consider our own prediction via pred_gff, and use<br></blockquote><blockquote type="cite">augustus and gene mark (with our training model). And i was able to use<br></blockquote><blockquote type="cite">altest and protein evidences. Maker happily picks one gene model when<br></blockquote><blockquote type="cite">there is a overlap between three different predictions. But, when I look<br></blockquote><blockquote type="cite">at the gff, it seems like it picks a gene model only when there is an<br></blockquote><blockquote type="cite">est/protein evidence. It leaves out some genes even though, they are<br></blockquote><blockquote type="cite">predicted by all three algorithms. Of course, keep_pred=1 helps to keep<br></blockquote><blockquote type="cite">all the models. This kind of leads to over prediction.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">But, I am looking for something in between. And would like to know if<br></blockquote><blockquote type="cite">that is possible?<br></blockquote><blockquote type="cite">1) Pick a gene model if it has an evidence from (est/prot etc...)<br></blockquote><blockquote type="cite">irrespective of how many algorithms predicted it<br></blockquote><blockquote type="cite">2) In the absence of extrinsic evidence (est/prot etc), pick a gene model<br></blockquote><blockquote type="cite">if that is predicted by at least two algorithms.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Or even simpler:<br></blockquote><blockquote type="cite">I have ab-initio predictions from three algorithms, Can I output, those<br></blockquote><blockquote type="cite">genes that is supported by at least two of them. I care less about<br></blockquote><blockquote type="cite">exactness of gene boundaries.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks,<br></blockquote><blockquote type="cite">Gowthaman<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">PS: With my recent attempts, i learned couple things about maker/other<br></blockquote><blockquote type="cite">associated tools that is not documented in gmod-maker wiki. Is it<br></blockquote><blockquote type="cite">possible/ok if I add contents to it. I am okay with running it by you<br></blockquote><blockquote type="cite">before making it public.<br></blockquote><br><span><gff3_preds2models></span>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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