FW: protein2genome gene models

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FW: protein2genome gene models

Carson Hinton Holt


From: Sivaranjani Namasivayam <[hidden email]>
Date: Wednesday, April 30, 2014 at 8:45 AM
To: "[hidden email]" <[hidden email]>
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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Re: FW: protein2genome gene models

Carson Holt-2
Make sure you're using the current version of MAKER.  It works on eukaryotes as well.

--Carson


From: Carson Holt <[hidden email]>
Date: Wednesday, April 30, 2014 at 8:53 AM
To: "[hidden email]" <[hidden email]>
Subject: [maker-devel] FW: protein2genome gene models



From: Sivaranjani Namasivayam <[hidden email]>
Date: Wednesday, April 30, 2014 at 8:45 AM
To: "[hidden email]" <[hidden email]>
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 [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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Re: 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 <[hidden email]> on behalf of Carson Holt <[hidden email]>
Sent: Wednesday, April 30, 2014 10:55 AM
To: Carson Holt; [hidden email]
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 <[hidden email]>
Date: Wednesday, April 30, 2014 at 8:53 AM
To: "[hidden email]" <[hidden email]>
Subject: [maker-devel] FW: protein2genome gene models



From: Sivaranjani Namasivayam <[hidden email]>
Date: Wednesday, April 30, 2014 at 8:45 AM
To: "[hidden email]" <[hidden email]>
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 [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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Re: FW: protein2genome gene models

Carson Holt-2
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 <[hidden email]>
Date: Thursday, May 15, 2014 at 1:00 PM
To: Carson Holt <[hidden email]>, Carson Holt <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]> on behalf of Carson Holt <[hidden email]>
Sent: Wednesday, April 30, 2014 10:55 AM
To: Carson Holt; [hidden email]
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 <[hidden email]>
Date: Wednesday, April 30, 2014 at 8:53 AM
To: "[hidden email]" <[hidden email]>
Subject: [maker-devel] FW: protein2genome gene models



From: Sivaranjani Namasivayam <[hidden email]>
Date: Wednesday, April 30, 2014 at 8:45 AM
To: "[hidden email]" <[hidden email]>
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 [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org