[maker-devel] FW: protein2genome gene models

[Carson Holt]

Upgrade to  2.31.5.

Changes since 2.31.3
*a protein2genome issue that was introduced in 2.31.3 was fixed
*fasta_merge failing with trnascan results issue was fixed
*other_gff input resulting in ARRAY reference being printed was fixed.
*naming of tRNA genes was improved to include amino acid identity

--Carson



From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Thursday, May 15, 2014 at 1:00 PM
To:  Carson Holt <carsonhh at gmail.com>, Carson Holt
<carson.holt at genetics.utah.edu>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject:  RE: [maker-devel] FW: protein2genome gene models

Hi Carson,



I upgraded to the MAKER version 2.31.3 (from MAKER 2.10). I want to predict
gene models directly from proteins. I provided proteins from a related
organism as input and set protein2genome to 1. However I do not get any gene
models predicted. 

I also tried this by using a transcriptome data set in addition to the
protein dataset and set est2genome and protein2genome to 1. I get gene
models from the transcripts but not proteins. When I look at the alignment
of the proteins on the genome, they seem to be aligning rather well and I
would expect to see a gene model predicted.

Would you know why this might be?



Also the number of gene models predicted (directly from the transriptome)in
this version is lower than the previous version I was using (MAKER 2.10). I
did notice this version is not predicting overlapping gene models, but that
is not rule.



Thanks,

Ranjani

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Carson
Holt <carsonhh at gmail.com>
Sent: Wednesday, April 30, 2014 10:55 AM
To: Carson Holt; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] FW: protein2genome gene models
 
Make sure you're using the current version of MAKER.  It works on eukaryotes
as well.

--Carson


From: Carson Holt <carson.holt at genetics.utah.edu>
Date: Wednesday, April 30, 2014 at 8:53 AM
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [maker-devel] FW: protein2genome gene models



From: Sivaranjani Namasivayam <ranjani at uga.edu>
Date: Wednesday, April 30, 2014 at 8:45 AM
To: "maker-devel-bounces at yandell-lab.org"
<maker-devel-bounces at yandell-lab.org>
Subject: protein2genome gene models

Hi,



I want to examine the gene models predicted diectly from protein data for my
genome.

MAKER has an option for this in the maker_opts.ctl file: protein2genome =1 ,
but it says for prokaryotes only.



Will this not work for eukaryotes? Is it because of introns?



Thanks,

Ranjani
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