[maker-devel] protein2genome question

[Mark Yandell]

Hi Brant,

Send us an example(s) gff3 and we will have a look. Often what's going on in these cases is its a pseudogene or low complexity hit, but bugs do happen.

cheers,

--mark

Mark Yandell
Associate Professor of Human Genetics
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: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Brant Peterson [brantp at gmail.com]
Sent: Thursday, April 09, 2009 6:00 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] protein2genome question

Maker folks,

I'm seeing some fairly real-looking hits turning up in protein2genome
results that aren't being put together and promoted to 'maker' gene
annotations, and I was wondering if there's a setting in maker
somewhere to do so.  It seems straightforward to hack this on ex post
facto, something like "take all protein2fasta hits, and make a new
parent gene with hits as exons if hits are to the same protein and
consecutive", but it seems like the sort of thing that maker probably
already does, and I just don't have it configured properly.

Thank you for your help!
-Brant

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