<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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).<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 19, 2017, at 6:47 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">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. <br class=""><br class=""></div>Thank you.<br class=""><br class=""></div>Best<br class=""></div>Quanwei<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-09-19 8:29 GMT-04:00 Daniel Ence <span dir="ltr" class=""><<a href="mailto:dandence@gmail.com" target="_blank" class="">dandence@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Quanwei,<br class="">
<br class="">
Increasing the “min_protein" parameter should get ride of those very short predicted proteins.<br class="">
<div class=""><div class="h5"><br class="">
<br class="">
<br class="">
> On Sep 19, 2017, at 12:14 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:<br class="">
><br class="">
> Hello:<br class="">
><br class="">
> I am working on a rodent species and get 28k annotated genes, I wonder whether you have any suggestions about the "min_protein" parameter?<br class="">
><br class="">
> I did not change the parameter in my current annotation. I get several very short predicted proteins (even those with only 1 amino acid).<br class="">
><br class="">
> min_protein=0 #require at least this many amino acids in predicted proteins<br class="">
><br class="">
> Thanks<br class="">
><br class="">
> Best<br class="">
> Quanwei<br class="">
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