[maker-devel] protein2genome gene models from protein gff

[Carson Holt]

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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