<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 maker_functional_gff and maker_functional_fasta scripts pull specific fields out of the UniProt fasta header, so they are tied to the format used by UniProt/Swiss-Prot. At one time I had modified them to also work with NR, but that was several years ago, so I don’t know if it would still work.<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 May 3, 2017, at 1:10 PM, Nathan Ricks <<a href="mailto:nathan.ricks@gmail.com" class="">nathan.ricks@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Is it possible to make my own database from sequences that I have downloaded form NCBI instead of using the UniProt/Swiss-Prot?</div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, May 3, 2017 at 10:30 AM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Use blastp with the the tab delimited format option and the UniProt/Swiss-Prot database. What additional filters you choose to set (i.e. e-value limit) may vary, although I would recommend 1e-6 or lower.<br class="">
<br class="">
—Carson<br class="">
<div class=""><div class="h5"><br class="">
> On May 3, 2017, at 10:19 AM, Nathan Ricks <<a href="mailto:nathan.ricks@gmail.com" class="">nathan.ricks@gmail.com</a>> wrote:<br class="">
><br class="">
> Hi,<br class="">
> I've been running your Maker pipeline, and I've reached Post Processing of Annotations portion. In your Online training you use the output.blastp and the outuput.iprscan files to help assign function.<br class="">
> My question is what format do these files need to be in.<br class="">
> Iprscan can produce files in a variety of formats: tsv, xml, gff3, html and SVG<br class="">
> while blastp can produce the tabular, pairise, xml and a number of others.<br class="">
><br class="">
> Thanks<br class="">
><br class="">
> Nathan Ricks<br class="">
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