[maker-devel] protein2genome question

[Brant Peterson]

Mark,

I doubt this is a bug, I think it's probably a threshold somewhere
that I need to tweak a little, or just an option I haven't got turned
on...
So, the example (ex.gff) I've sent you is all lines of type maker,
est2genome and protein2genome from a round of annotation on a BAC I've
been using for testing.  The maker annotation found is correct, but
two protein2genome hits are also correct (exons of the same gene).
These are the Asip hits (Name=sp|Q1XGU5|ASIP_COLPO).

As an unrelated question, how do the "est_reads" and "altest" options
work? (these are new since the last version of maker I used, and seem
pretty exciting!)

Thank you again for your help,
Brant

On Thu, Apr 9, 2009 at 8:14 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
> 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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>
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