[maker-devel] about min_protein

[Carson Holt]

The value is arbitrary, but some submission databases like NCBI will flag entries under ~20-30 amino acids as errors if you try and submit them (I can’t remember the exact number).

—Carson



> On Sep 19, 2017, at 6:47 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Thank you Daniel. I wonder whether there is a suggested value for the “min_protein" parameter (e.g., 20 amino acid, 50 amino acid?), that people often use. I am studying a rodent species. 
> 
> Thank you.
> 
> Best
> Quanwei
> 
> 2017-09-19 8:29 GMT-04:00 Daniel Ence <dandence at gmail.com <mailto:dandence at gmail.com>>:
> Hi Quanwei,
> 
> Increasing the “min_protein" parameter should get ride of those very short predicted proteins.
> 
> 
> 
> > On Sep 19, 2017, at 12:14 AM, Quanwei Zhang <qwzhang0601 at gmail.com <mailto:qwzhang0601 at gmail.com>> wrote:
> >
> > Hello:
> >
> > I am working on a rodent species and get 28k annotated genes, I wonder whether you have any suggestions about the "min_protein" parameter?
> >
> > I did not change the parameter in my current annotation. I get several very short predicted proteins (even those with only 1 amino acid).
> >
> > min_protein=0 #require at least this many amino acids in predicted proteins
> >
> > Thanks
> >
> > Best
> > Quanwei
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