[maker-devel] maker2 scripts for functional annotation

[Mark Yandell]

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 couldn’t 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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