<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><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> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, September 27, 2013 6:42 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:mhinsley@ebi.ac.uk">mhinsley@ebi.ac.uk</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] maker2 scripts for functional annotation<br></div><div><br></div><div><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 set keep_preds=1, then unsupported predictions become genes (you don't need EST's or proteins). If you only supply a single pred_gff input and turn everything else off, then the result is maker turning match/match_part into gene/mRNA/exon/CDS, and it runs rather quickly (only processing is the time spent verifying reading frame, etc.). If you leave other things on in the control files, then you will get a lot of other processes like a standard MAKER run.</div><div><br></div><div>Thanks,</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> <<a href="mailto:mhinsley@ebi.ac.uk">mhinsley@ebi.ac.uk</a>><br><span style="font-weight:bold">Date: </span> Friday, September 27, 2013 4:34 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">Subject: </span> Re: [maker-devel] maker2 scripts for functional annotation<br></div><div><br></div><div dir="ltr">Hi... Xia and Carson<br><br>I've been trying to do something similar to get maker gene models derived from CEGMA predictions, and thought it would be nice to use the CEGMA GFF rather than the protein fasta as that includes exon structure. The CEGMA output is a GFFv2 variant and i managed to get this into GFFv3 via a combination of Augustus/gff2gbSmallDNA.pl, EMBOSS/seqret and then sed to patch a few tags. (the tags came out as into EMBL/ databank_entry, mRNA and CDS, not sure if this is valid for pred_gff or not))<br><br>If you run maker with pref_gff=my_file and keep pred=1 with est2genome and protien2genome switched off then you get a lot of est2genome and blast activity. (I also had pred_stats=1 on one run). You can prevent most of this my removing the est and protein files from the config :-). However without EST and protien evidence you get no gene models, so (i guess - I'm new to maker also, Carson please correct me if i'm wrong) if you've already run est2genome and proetien2genome then pref_gff could be used to convert your GFF to maker models, if you filter the maker gene models by source.<br><br>AFAICS if you have est and protein data configured and est2genome and protein2genome switched off then maker will used these as evidence for your GFF which means it will have to align them, which could be mistaken for running those analyses.<br><br>Hope this helps and apologies if i'm wrong!<br><code class="java plain"><br></code><br>On Wednesday, 25 September 2013 15:35:46 UTC+1, Carson Holt wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">If it is launching predictors then you have snap hmm or augustus_species<br>set. You ned to blank out all other options in the control files<br>(including repeat masking options, proteins, ESTs, etc.) when trying to<br>convert mathc/match_part to gene/mRNA/exons/CDS, or else those other<br>programs will run.<p>--Carson</p><p><br>On 9/25/13 10:31 AM, "<a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">Xia...@dupont.com</a>" <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">Xia...@dupont.com</a>> wrote:</p><p>>Hi Carson,<br>><br>>Thank you for the message and your kind help. We tested maker2 by setting<br>>keep_preds=1, pred_gff=generated_gff_file_<wbr>from_first_makerRun . But it<br>>seemed maker2 started to launch all predictors again and it took long<br>>time to finish. I wonder if there is any way that we can directly get<br>>gene/mRNA/exons/CDS gff file without re-running maker2 to convert<br>>match/match_part features into gene/mRNA/exons/CDS.<br>><br>>Thanks,<br>>Xia<br>><br>>-----Original Message-----<br>>From: Carson Holt [mailto:<a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">cars...@gmail.com</a>]<br>>Sent: Thursday, September 19, 2013 5:58 PM<br>>To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY;<br>><a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">maker...@yandell-lab.org</a><br>>Subject: Re: [maker-devel] maker2 scripts for functional annotation<br>><br>>Hello Corban & Xia,<br>><br>>Some scripts like gff3_preds2models are deprecated. To get the same<br>>result as was offered by gff3_preds2models, just give your<br>>match/match_part features to pref_gff= in the maker_opts.ctl file, set<br>>keep_preds=1, and run with all other options and predictors turned off.<br>>The final MAKER result will be your match/match_part features converted<br>>into gene/mRNA/exons/CDS.<br>><br>>For functional annotation, you can use Interproscan, BLASTP against<br>>UniProt, or BALST2GO. My preference is to use InterProScan to add GO<br>>terms and proteins domains via the ipr_update_gff and iprscan2gff3<br>>scripts. Then add putative gene functions via BLASTP to UniProt and<br>>maker_functional_fasta and maker_functional_gff scripts.<br>><br>>Go ahead and take a look and that those tools and let me know if you have<br>>any questions or need help you configuring them.<br>><br>>Thanks,<br>>Carson<br>><br>><br>>On 9/19/13 11:53 AM, "Mark Yandell" <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">myan...@genetics.utah.edu</a>> wrote:<br>><br>>>Hi Corban & Xia,<br>>><br>>><br>>>I've forwarded your question along to the MAKER_dev list, were you can<br>>>get speedy answers to your maker related questions. Thanks for using<br>>>MAKER.<br>>><br>>>--mark<br>>><br>>><br>>>Mark Yandell<br>>>Professor of Human Genetics<br>>>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of<br>>>Human Genetics University of Utah<br>>>15 North 2030 East, Room 2100<br>>>Salt Lake City, UT 84112-5330<br>>>ph:801-587-7707<br>>><br>>>____________________________<wbr>____________<br>>>From: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">Xia...@dupont.com</a> [<a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">Xia...@dupont.com</a>]<br>>>Sent: Thursday, September 19, 2013 11:49 AM<br>>>To: Mark Yandell; <a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">Corban-Gre...@dupont.<wbr>com</a><br>>>Subject: maker2 scripts for functional annotation<br>>><br>>>Dr. Yandell,<br>>><br>>>We were recently evaluating maker2 for annotation and going through the<br>>>maker tutorial from 2012.<br>>><br>>><a href="http://gmod.org/wiki/MAKER_Tutorial_2012" target="_blank">http://gmod.org/wiki/MAKER_<wbr>Tutorial_2012</a><br>>><br>>>The tutorial makes references to some scripts that we couldn©öt find in<br>>>the current release. We were looking for scripts like<br>>>gff3_preds2models to convert match/match_part format into annotations<br>>>with gene/mRNA/exons/CDS and others. I was wondering if maybe we did<br>>>not have the most up to date version.<br>>><br>>>In addition to getting accurate gene annotations, I was looking for a<br>>>solution to get functional assignments. I see that there are some<br>>>scripts like maker_functional_fasta that may help, but I was wondering<br>>>what you would recommend.<br>>><br>>>Thanks,<br>>><br>>>Corban & Xia<br>>><br>>>This communication is for use by the intended recipient and contains<br>>>information that may be Privileged, confidential or copyrighted under<br>>>applicable law. If you are not the intended recipient, you are hereby<br>>>formally notified that any use, copying or distribution of this e-mail,<br>>>in whole or in part, is strictly prohibited. Please notify the sender<br>>>by return e-mail and delete this e-mail from your system. 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This e-mail does not constitute a<br>>>consent to the use of sender's contact information for direct marketing<br>>>purposes or for transfers of data to third parties.<br>>><br>>>The <a href="http://dupont.com" target="_blank">dupont.com</a> web address will continue in use for a transitional<br>>>period for communications sent or received on behalf of DuPont<br>>>Performance Coatings., which is not affiliated in any way with the<br>>>DuPont Company.<br>>><br>>>Francais Deutsch Italiano Espanol Portugues Japanese Chinese<br>>>Korean<br>>><br>>> <a href="http://www.DuPont.com/corp/email_disclaimer.html" target="_blank">http://www.DuPont.com/corp/<wbr>email_disclaimer.html</a><br>>><br>>>____________________________<wbr>___________________<br>>>maker-devel mailing list<br>>><a href="javascript:" target="_blank" gdf-obfuscated-mailto="i3Jbyhl9MT0J">maker...@box290.bluehost.<wbr>com</a><br>>><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/<wbr>mailman/listinfo/maker-devel_<wbr>yandell-lab.org</a><br>><br>><br>><br>>This communication is for use by the intended recipient and contains<br>>information that may be Privileged, confidential or copyrighted under<br>>applicable law. 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