[maker-devel] maker2 scripts for functional annotation

[Xia.Cao at dupont.com]

Hi Carson,

Thank you for the message and your kind help. We tested maker2 by setting keep_preds=1, pred_gff=generated_gff_file_from_first_makerRun . But it seemed maker2 started to launch all predictors again and it took long time to finish. I wonder if there is any way that we can directly get gene/mRNA/exons/CDS gff file without re-running maker2 to convert match/match_part features into gene/mRNA/exons/CDS. 

Thanks,
Xia

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, September 19, 2013 5:58 PM
To: Mark Yandell; CAO, XIA; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] maker2 scripts for functional annotation

Hello Corban & Xia,

Some scripts like gff3_preds2models are deprecated.  To get the same result as was offered by gff3_preds2models, just give your match/match_part features to pref_gff= in the maker_opts.ctl file, set keep_preds=1, and run with all other options and predictors turned off.
The final MAKER result will be your match/match_part features converted into gene/mRNA/exons/CDS.

For functional annotation, you can use Interproscan, BLASTP against UniProt, or BALST2GO.  My preference is to use InterProScan to add GO terms and proteins domains via the ipr_update_gff and iprscan2gff3 scripts.  Then add putative gene functions via BLASTP to UniProt and maker_functional_fasta and maker_functional_gff scripts.

Go ahead and take a look and that those tools and let me know if you have any questions or need help you configuring them.

Thanks,
Carson


On 9/19/13 11:53 AM, "Mark Yandell" <myandell at genetics.utah.edu> wrote:

>Hi  Corban & Xia,
>
>
>I've forwarded your question along to the MAKER_dev list, were you can 
>get speedy answers to your maker related questions. Thanks for using 
>MAKER.
>
>--mark
>
>
>Mark Yandell
>Professor of Human Genetics
>H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of 
>Human Genetics University of Utah
>15 North 2030 East, Room 2100
>Salt Lake City, UT 84112-5330
>ph:801-587-7707
>
>________________________________________
>From: Xia.Cao at dupont.com [Xia.Cao at dupont.com]
>Sent: Thursday, September 19, 2013 11:49 AM
>To: Mark Yandell; Corban-Gregory.Rivera at dupont.com
>Subject: maker2 scripts for functional annotation
>
>Dr. Yandell,
>
>We were recently evaluating maker2 for annotation and going through the 
>maker tutorial from 2012.
>
>http://gmod.org/wiki/MAKER_Tutorial_2012
>
>The tutorial makes references to some scripts that we couldn¹t find in 
>the current release.  We were looking for scripts like 
>gff3_preds2models to convert match/match_part format into annotations 
>with gene/mRNA/exons/CDS and others.  I was wondering if maybe we did 
>not have the most up to date version.
>
>In addition to getting accurate gene annotations, I was looking for a 
>solution to get functional assignments.  I see that there are some 
>scripts like maker_functional_fasta that may help, but I was wondering 
>what you would recommend.
>
>Thanks,
>
>Corban & Xia
>
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