[maker-devel] maker2 scripts for functional annotation

[Carson Holt]

If it is launching predictors then you have snap hmm or augustus_species
set.  You ned to blank out all other options in the control files
(including repeat masking options, proteins, ESTs, etc.) when trying to
convert mathc/match_part to gene/mRNA/exons/CDS, or else those other
programs will run.

--Carson


On 9/25/13 10:31 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>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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