<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Xia,<div><br></div><div>You can use EST evidence from other strains/species. The considerations are as follows: When you pass EST (or mRNASeq based transcripts) evidence MAKER uses blastn to align those with alignment parameters that assume they sequences will align easily with almost perfect identity - this is fast. If you use EST/mRNA evidence from another species MAKER uses tblastx to compare the RNA evidence to the assembly, both translated into protein space - this works fine, but it is slow and often doesn't get you much more evidence than you could have gotten from proteins as evidence. If you believe that you're other strain should have very little divergence in sequence at the nt level then you could experiment with passing EST/mRNA evidence as est in the control file. Consider this an experiment, do it on a few contigs and examine the results carefully and skeptically. If it works well, that would be the way to go because you've get better UTRs, but if it doesn't you'll see that you get little support for models because sequence divergence was too much for good alignment. In that case you'll need to use alt_est and this will be slower and you'll likely get little in the way of support for UTRs - in this case as well, do a few contigs and examine the output carefully to see if the additional alignment time with tblastx is worth it in your case.</div><div><br></div><div>Barry</div><div><div><br></div><div><br></div><div><div>On Oct 2, 2013, at 8:40 AM, <<a href="mailto:Xia.Cao@dupont.com">Xia.Cao@dupont.com</a>></div><div> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Carson,<br><br>Thank you for your quick and kind reply. One more question here. If we don't have EST evidence for the strain we sequenced/assembled, will it be ok to provide some EST evidence that is from some other strains which are close to the one we are trying to annotate? Could you please let us know how this will affect performance of maker2?<br><br>Thank you again.<br><br>Best,<br>Xia<br><br>-----Original Message-----<br>From: Carson Holt [mailto:carsonhh@gmail.com] <br>Sent: Wednesday, October 02, 2013 10:15 AM<br>To: CAO, XIA<br>Cc: <a href="mailto:myandell@genetics.utah.edu">myandell@genetics.utah.edu</a>; RIVERA, CORBAN GREGORY; <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br>Subject: Re: [maker-devel] maker2 scripts for functional annotation<br><br>It still works, but it will be reduced. Without ESTs you won't get any UTR prediction, also you will be limited by how well the protein set matches to the genes. If you use the protein set of a close relative you will capture most things. You will probably capture 80-95% of what you would by also including ESTs. It all depending on how different the species in the proteins evidence file are compared to the the species being annotated.<br><br>--Carson<br><br>On 10/1/13 3:00 PM, "<a href="mailto:Xia.Cao@dupont.com">Xia.Cao@dupont.com</a>" <<a href="mailto:Xia.Cao@dupont.com">Xia.Cao@dupont.com</a>> wrote:<br><br><blockquote type="cite">Hi Carson,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thank you for your message and your kind help. Now conversion from <br></blockquote><blockquote type="cite">match/match_part to gene/mRNA/exons/CDS works well after blanking out <br></blockquote><blockquote type="cite">some options in control file.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have one more question about maker2. In case we don't have EST <br></blockquote><blockquote type="cite">evidence (set of ESTs or assembled mRNA-seq in fasta format) for a <br></blockquote><blockquote type="cite">genome, does<br></blockquote><blockquote type="cite">maker2 function? If it does function, could you please let me know the <br></blockquote><blockquote type="cite">performance of maker2 without providing EST evidence compared to the <br></blockquote><blockquote type="cite">one with EST evidence?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thank you again and I look forward to hearing from you.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite">Xia<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----Original Message-----<br></blockquote><blockquote type="cite">From: Carson Holt [mailto:carsonhh@gmail.com]<br></blockquote><blockquote type="cite">Sent: Wednesday, September 25, 2013 10:36 AM<br></blockquote><blockquote type="cite">To: CAO, XIA; <a href="mailto:myandell@genetics.utah.edu">myandell@genetics.utah.edu</a>; RIVERA, CORBAN GREGORY; <br></blockquote><blockquote type="cite"><a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br></blockquote><blockquote type="cite">Subject: Re: [maker-devel] maker2 scripts for functional annotation<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">If it is launching predictors then you have snap hmm or <br></blockquote><blockquote type="cite">augustus_species set. You ned to blank out all other options in the <br></blockquote><blockquote type="cite">control files (including repeat masking options, proteins, ESTs, etc.) <br></blockquote><blockquote type="cite">when trying to convert mathc/match_part to gene/mRNA/exons/CDS, or else <br></blockquote><blockquote type="cite">those other programs will run.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--Carson<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 9/25/13 10:31 AM, "<a href="mailto:Xia.Cao@dupont.com">Xia.Cao@dupont.com</a>" <<a href="mailto:Xia.Cao@dupont.com">Xia.Cao@dupont.com</a>> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi Carson,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thank you for the message and your kind help. We tested maker2 by <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun .<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">But it seemed maker2 started to launch all predictors again and it <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">took long time to finish. I wonder if there is any way that we can <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">directly get gene/mRNA/exons/CDS gff file without re-running maker2 to <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">convert match/match_part features into gene/mRNA/exons/CDS.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Xia<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-----Original Message-----<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">From: Carson Holt [mailto:carsonhh@gmail.com]<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Sent: Thursday, September 19, 2013 5:58 PM<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Subject: Re: [maker-devel] maker2 scripts for functional annotation<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Hello Corban & Xia,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Some scripts like gff3_preds2models are deprecated. To get the same <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">result as was offered by gff3_preds2models, just give your <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">match/match_part features to pref_gff= in the maker_opts.ctl file, set <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">keep_preds=1, and run with all other options and predictors turned off.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">The final MAKER result will be your match/match_part features <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">converted into gene/mRNA/exons/CDS.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">For functional annotation, you can use Interproscan, BLASTP against <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">UniProt, or BALST2GO. My preference is to use InterProScan to add GO <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">terms and proteins domains via the ipr_update_gff and iprscan2gff3 <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">scripts. Then add putative gene functions via BLASTP to UniProt and <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">maker_functional_fasta and maker_functional_gff scripts.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Go ahead and take a look and that those tools and let me know if you <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">have any questions or need help you configuring them.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Carson<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On 9/19/13 11:53 AM, "Mark Yandell" <<a href="mailto:myandell@genetics.utah.edu">myandell@genetics.utah.edu</a>> wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Corban & Xia,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I've forwarded your question along to the MAKER_dev list, were you <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">can get speedy answers to your maker related questions. Thanks for <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">using MAKER.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">--mark<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Mark Yandell<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Professor of Human Genetics<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Human Genetics University of Utah<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">15 North 2030 East, Room 2100<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Salt Lake City, UT 84112-5330<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">ph:801-587-7707<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">________________________________________<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">From: <a href="mailto:Xia.Cao@dupont.com">Xia.Cao@dupont.com</a> [<a href="mailto:Xia.Cao@dupont.com">Xia.Cao@dupont.com</a>]<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Sent: Thursday, September 19, 2013 11:49 AM<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">To: Mark Yandell; <a href="mailto:Corban-Gregory.Rivera@dupont.com">Corban-Gregory.Rivera@dupont.com</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Subject: maker2 scripts for functional annotation<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dr. Yandell,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">We were recently evaluating maker2 for annotation and going through <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the maker tutorial from 2012.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://gmod.org/wiki/MAKER_Tutorial_2012">http://gmod.org/wiki/MAKER_Tutorial_2012</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The tutorial makes references to some scripts that we couldnąt find <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">in the current release. We were looking for scripts like <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">gff3_preds2models to convert match/match_part format into annotations <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">with gene/mRNA/exons/CDS and others. I was wondering if maybe we did <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">not have the most up to date version.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">In addition to getting accurate gene annotations, I was looking for a <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">solution to get functional assignments. I see that there are some <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">scripts like maker_functional_fasta that may help, but I was <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">wondering what you would recommend.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Corban & Xia<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">This communication is for use by the intended recipient and contains <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">information that may be Privileged, confidential or copyrighted under <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">applicable law. 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<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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