about min_protein

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about min_protein

Quanwei Zhang
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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Re: about min_protein

Daniel Ence-2
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 <[hidden email]> 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
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: about min_protein

Quanwei Zhang
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 <[hidden email]>:
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 <[hidden email]> 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
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



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Re: about min_protein

Carson Holt-2
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 <[hidden email]> 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 <[hidden email]>:
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 <[hidden email]> 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
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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


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