[maker-devel] FW: protein2genome gene models

[Sivaranjani Namasivayam]

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



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

_______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140515/95976492/attachment-0002.html>