[maker-devel] maker2 scripts for functional annotation

Wed Oct 2 08:14:44 MDT 2013

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
>>>
>>>This communication is for use by the intended recipient and contains
>>>information that may be Privileged, confidential or copyrighted under
>>>applicable law. If you are not the intended recipient, you are hereby
>>>formally notified that any use, copying or distribution of this
>>>e-mail, in whole or in part, is strictly prohibited. Please notify the
>>>sender by return e-mail and delete this e-mail from your system.
>>>Unless explicitly and conspicuously designated as "E-Contract
>>>Intended", this e-mail does not constitute a contract offer, a
>>>contract amendment, or an acceptance of a contract offer. This e-mail
>>>does not constitute a consent to the use of sender's contact
>>>information for direct marketing purposes or for transfers of data to
>>>third parties.
>>>
>>>The dupont.com web address will continue in use for a transitional
>>>period for communications sent or received on behalf of DuPont
>>>Performance Coatings., which is not affiliated in any way with the
>>>DuPont Company.
>>>
>>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>>Korean
>>>
>>>          http://www.DuPont.com/corp/email_disclaimer.html
>>>
>>>_______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>g
>>
>>
>>
>>This communication is for use by the intended recipient and contains
>>information that may be Privileged, confidential or copyrighted under
>>applicable law. If you are not the intended recipient, you are hereby
>>formally notified that any use, copying or distribution of this e-mail,
>>in whole or in part, is strictly prohibited. Please notify the sender
>>by return e-mail and delete this e-mail from your system. Unless
>>explicitly and conspicuously designated as "E-Contract Intended", this
>>e-mail does not constitute a contract offer, a contract amendment, or
>>an acceptance of a contract offer. This e-mail does not constitute a
>>consent to the use of sender's contact information for direct marketing
>>purposes or for transfers of data to third parties.
>>
>>The dupont.com<http://dupont.com/> web address will continue in use for
>>a transitional period for communications sent or received on behalf of
>>DuPont Performance Coatings., which is not affiliated in any way with
>>the DuPont Company.
>>
>>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
>>Korean
>>
>>           http://www.DuPont.com/corp/email_disclaimer.html
>>
>
>
>
>This communication is for use by the intended recipient and contains
>information that may be Privileged, confidential or copyrighted under
>applicable law. If you are not the intended recipient, you are hereby
>formally notified that any use, copying or distribution of this e-mail,
>in whole or in part, is strictly prohibited. Please notify the sender by
>return e-mail and delete this e-mail from your system. Unless explicitly
>and conspicuously designated as "E-Contract Intended", this e-mail does
>not constitute a contract offer, a contract amendment, or an acceptance
>of a contract offer. This e-mail does not constitute a consent to the
>use of sender's contact information for direct marketing purposes or for
>transfers of data to third parties.
>
>The dupont.com<http://dupont.com/> web address will continue in use for a
>transitional period for communications sent or received on behalf of
>DuPont
>Performance Coatings., which is not affiliated in any way with the DuPont
>Company.
>
>Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese  Korean
>
>           http://www.DuPont.com/corp/email_disclaimer.html
>