[maker-devel] what is a 'model file' for the web annotation service?

[Jason Stajich]

the parameters.tar.gz should contain this. - untar in the species folder in
you local Augustus install or set the Augustus config env variable to point
to a personal copy of the Augustus config folder and put this there.
Whatever you name this parameters folder is the species name you put in the
maker config.

On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu> wrote:

> Sorry if this is a dumb question.
>
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model
> file' as input
>
> I generated a  training set of genes from my species through use of online
> AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
> input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
> sequences,and a set of protein sequences from those cDNAs, for the species.
> I received these files (folders) back from the AUGUSTUS server (in addition
> to log and err files):
>
>
> *Species parameter archive*:  parameters.tar.gz
>
> *Training genes: * training.gb.gz
>
> *Ab initio predictions*:  ab_initio.tar.gz
>
> *predictions with hints:*  hints_pred.tar.gz
>
>
>
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
> train itself. The format is Genbank.
>
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
> folders), 1 gff and 1 gtf.
>
> Do you know which file would be correct for input to online MAKER as a
> 'model' file?
>
>
> (NB there is no UTR predictions file, as my input cDNAs did not have
> enough UTR information in them )
>
>
>
>
>
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