[maker-devel] FW: MAKER Genes Correspondence Question

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Mark Yandell

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Aug 3, 2011, 3:48:24 PM8/3/11

to maker...@yandell-lab.org, Carson Holt

________

Hey Carson,

can you get back to Deepthika on this?

thanks,

--mark

From: enna...@onid.orst.edu [enna...@onid.orst.edu]
Sent: Wednesday, August 03, 2011 12:13 PM
To: Mark Yandell
Subject: MAKER Genes Correspondence Question

To whom it may concern,
Recently, we used MAKER to passage an older version of the
Phytophthora sojae genome annotation (v1.1) to a new version of the
genome. Due to how different these assemblies are, we had difficulty
using an assembly based annotation program. However, using the FASTA
cDNA sequences in MAKER worked well.

One issue, we would like to know/figure out/understand is which
original gene sequences correspond to the new maker genes.
Is there a way to tell which new genes correspond to the original genes?

We were unable to find anything in your GMOD and I was wondering if
you would be able to address this question. If you could get back to
me as soon as you can, that would be greatly appreciated.

Please feel free to contact me at enna...@onid.orst.edu.

Thank you,

Deepthika Ennamuri
Oregon State University

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Carson Holt

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Aug 3, 2011, 3:59:00 PM8/3/11

to Mark Yandell, maker...@yandell-lab.org

You can use the map2assembly tool bundled with MAKER, or add the following
line to the end of the maker_opts.ctl file.

est_forward=1

This is sort of a quirky way to cause MAKER to run the same as map2assembly
(They are basically the same programs under the hood). Scan the output GFF3
to see if any old genes map to more than one location. I haven't built in a
mechanism to auto-disambiguate yet in those case, so you will be presented
with all options to review manually.