[maker-devel] protein2genome gene models from protein gff

[Carson Holt]

That's what I'd do.  But really protein2genome=1 is just meant to get enough
rough gene models to train a gene predictor.  You don't need to run it
across the whole genome.  But if you do, when you run again after training
the gene predictor, MAKER will detect the old BLAST jobs and they won't have
to rerun on the second MAKER run.

--Carson


From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Thursday, June 5, 2014 at 12:56 PM
To:  Carson Holt <carsonhh at gmail.com>
Subject:  RE: [maker-devel] protein2genome gene models from protein gff

So what would you suggest is the best way to get protein2genome predictions?
Use fasta sequences, instead of gff?



Thanks,

Ranjani

From: Carson Holt <carsonhh at gmail.com>
Sent: Thursday, June 05, 2014 2:08 PM
To: Sivaranjani Namasivayam; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] protein2genome gene models from protein gff
 
est_gff assumes the alignments are spliced correctly.  The protein2genome
option also makes that assumption but with a little less confidence that the
user always provides splice aware alignments, so in some instances (like
protein2genome=1) it may not pass them forward as guaranteed splice aware
alignments.

--Carson


From: Sivaranjani Namasivayam <ranjani at uga.edu>
Date: Thursday, June 5, 2014 at 9:49 AM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] protein2genome gene models from protein gff

Hi,



I am trying to predict gene models from protein evidence, using the
parameter protein2genome set to 1.



I get gene models predicted if I provide the proteins as a fasta file, but
not as gff (I want to use a gff format to avoid the blastx step again). Is
this expected?



In case of transcriptome evidence and est2genome set to 1, I get gene models
predicted with both fasta and gff formats.



Thanks,

Ranjani
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