[maker-devel] Post Processing of Annotations

[Carson Holt]

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.

—Carson



> On May 3, 2017, at 1:10 PM, Nathan Ricks <nathan.ricks at gmail.com> wrote:
> 
> Is it possible to make my own database from sequences that I have downloaded form NCBI instead of using the UniProt/Swiss-Prot?
> 
> On Wed, May 3, 2017 at 10:30 AM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> 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.
> 
> —Carson
> 
> > On May 3, 2017, at 10:19 AM, Nathan Ricks <nathan.ricks at gmail.com <mailto:nathan.ricks at gmail.com>> wrote:
> >
> > Hi,
> > 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.
> > My question is what format do these files need to be in.
> > Iprscan can produce files in a variety of formats: tsv, xml, gff3, html and SVG
> > while blastp can produce the tabular, pairise, xml and a number of others.
> >
> > Thanks
> >
> > Nathan Ricks
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> 
> 

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