Training Augustus

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Training Augustus

claudia

Hello,

  Thanks for the help with regards to training SNAP. I was wondering if Augustus is also trainable? Also,  what is the  recommended protocol with regards to training, i.e. is one trained ab-initio gene predictor sufficient?

Thanks in advance,
Claudia


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Re: Training Augustus

Carson Holt-2
Re: [maker-devel] Training Augustus Yes. Augustus is trainable.  You can either convert GFF3 annotations into GenBank format or just use ESTs as the basis for training (both methods are described to a degree in the Augustus documentation).

I would recommend training Augustus.  It can be difficult, but overall I’ve found that Augustus often outperforms SNAP, so adding it does improve annotations.

--Carson



On 7/27/11 2:13 PM, "Dinatale C" <dinatal@...> wrote:

Hello,

  Thanks for the help with regards to training SNAP. I was wondering if Augustus is also trainable? Also,  what is the  recommended protocol with regards to training, i.e. is one trained ab-initio gene predictor sufficient?

Thanks in advance,
Claudia


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Re: Training Augustus

Jason Stajich-4
Second on that.   I also have some scripts that help convert the intermediate training files that start from the export.zff you generate as part of the SNAP training into GenBank as the ZFF -> GenBank  seems to be still a bit tricky.

I end up converting ZFF to GFF2 and then I  run this through, but it took a little bit of wrangling to get this working and I *think* this script is generic enough but I haven't spent a lot of time trying to make sure this will work.
https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/snap_gff2augstus_gbk.pl

The scripts that come from Augustus seem to fail on the gff or gtf to genbank conversion in my experience.

Jason
On Jul 29, 2011, at 5:30 AM, Carson Holt wrote:

Yes. Augustus is trainable.  You can either convert GFF3 annotations into GenBank format or just use ESTs as the basis for training (both methods are described to a degree in the Augustus documentation).

I would recommend training Augustus.  It can be difficult, but overall I’ve found that Augustus often outperforms SNAP, so adding it does improve annotations.

--Carson



On 7/27/11 2:13 PM, "Dinatale C" <<a href="x-msg://85/dinatal@uwindsor.ca">dinatal@...> wrote:

Hello,

  Thanks for the help with regards to training SNAP. I was wondering if Augustus is also trainable? Also,  what is the  recommended protocol with regards to training, i.e. is one trained ab-initio gene predictor sufficient?

Thanks in advance,
Claudia


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