[maker-devel] maker2 scripts for functional annotation

Carson Holt carsonhh at gmail.com
Wed Oct 2 08:43:29 MDT 2013 

That's ok.  If it is very closely related, provide it directly to the est=
option, otherwise provide it to the altest= option.  The difference
between the two options is how they are aligned.  The altest= alignments
takes about 10x longer than the est= alignments.

--Carson


On 10/2/13 10:40 AM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:

>Hi Carson,
>
>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?
>
>Thank you again.
>
>Best,
>Xia
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Wednesday, October 02, 2013 10:15 AM
>To: CAO, XIA
>Cc: myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>
>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.
>
>--Carson
>
>On 10/1/13 3:00 PM, "Xia.Cao at dupont.com" <Xia.Cao at dupont.com> wrote:
>
>>Hi Carson,
>>
>>Thank you for your message and your kind help. Now conversion from
>>match/match_part to gene/mRNA/exons/CDS works well after blanking out
>>some options in control file.
>>
>>I have one more question about maker2. In case we don't have EST
>>evidence (set of ESTs or assembled mRNA-seq in fasta format) for a
>>genome, does
>>maker2 function? If it does function, could you please let me know the
>>performance of maker2 without providing EST evidence compared to the
>>one with EST evidence?
>>
>>Thank you  again and I look forward to hearing from you.
>>
>>Best,
>>Xia
>>
>>
>>
>>
>>-----Original Message-----
>>From: Carson Holt [mailto:carsonhh at gmail.com]
>>Sent: Wednesday, September 25, 2013 10:36 AM
>>To: CAO, XIA; myandell at genetics.utah.edu; RIVERA, CORBAN GREGORY;
>>maker-devel at yandell-lab.org
>>Subject: Re: [maker-devel] maker2 scripts for functional annotation
>>
>>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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>>>>g
>>>
>>>
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>>
>>
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>
>
>
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>DuPont
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