[maker-devel] maker2 scripts for functional annotation
Xia.Cao at dupont.com
Xia.Cao at dupont.com
Wed Oct 2 11:51:26 MDT 2013
Hi Barry,
Thank you very much for the message and suggestions. It's really helpful to us. We will do some tests to see how we can take advantage of Maker2 to produce high-quality gene models from our assembled genome.
Thank you again,
Xia
From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
Sent: Wednesday, October 02, 2013 1:21 PM
To: CAO, XIA
Cc: carsonhh at gmail.com; maker-devel at yandell-lab.org; RIVERA, CORBAN GREGORY
Subject: Re: [maker-devel] maker2 scripts for functional annotation
Hi Xia,
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.
Barry
On Oct 2, 2013, at 8:40 AM, <Xia.Cao at dupont.com<mailto: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<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY; maker-devel at yandell-lab.org<mailto: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<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto: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<mailto:myandell at genetics.utah.edu>; RIVERA, CORBAN GREGORY;
maker-devel at yandell-lab.org<mailto: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<mailto:Xia.Cao at dupont.com>" <Xia.Cao at dupont.com<mailto: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<mailto: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<mailto: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<mailto:Xia.Cao at dupont.com> [Xia.Cao at dupont.com<mailto:Xia.Cao at dupont.com>]
Sent: Thursday, September 19, 2013 11:49 AM
To: Mark Yandell; Corban-Gregory.Rivera at dupont.com<mailto: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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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
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(801) 585-3543
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