[maker-devel] maker2 scripts for functional annotation

[Carson Holt]

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.org