[maker-devel] Question on ESTs and functional annotations

[Shane Brubaker]

That is very helpful, thanks Barry!

-----Original Message-----
From: Barry Moore [mailto:barry.moore at genetics.utah.edu]
Sent: Monday, November 16, 2009 2:35 PM
To: Shane Brubaker
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Question on ESTs and functional annotations

Shane,

With regards to your second question...we've got a few scripts in the
bin directory that we have used to add functional annotations to MAKER
output.  They are:

maker_functional_fasta
maker_functional_gff
ipr_update_gff

The first two will take a blastp output from your MAKER proteins
against swissprot and add this sort of thing:

name:"Serine-aspartate repeat-containing protein I (Staphylococcus
saprophyticus)"
Note="Serine-aspartate repeat-containing protein I (Staphylococcus
saprophyticus)"

to your fasta and GFF files respectively.  It's not currently adding
the swissprot ID to that output, but it would be trivial to alter
either or both to do so.

Also a great (but CPU costly) way to get deeper functional annotations
is to run IPRscan on your MAKER proteins and then use the last script
mentioned above to add Dbxref and Ontology_term attributes to your GFF.

Have a look at those scripts and then holler back if you have any
questions or want more details.

Barry

On Nov 16, 2009, at 1:45 PM, Shane Brubaker wrote:

> Hi, I had a couple of general questions.
>
> 1.  What are the EST blastn results that are found in the MAKER gff3
> output?  I thought these might be a track of my ESTs mapped onto the
> genome, but they seem to contain pieces of the EST but not the
> entire thing?
> 2.  What is a good way to add functional annotation to the gene
> results? I have a track of protein matches, I used Swissprot as my
> set of proteins.  So I can see proteins and I can look up my
> Swissprot accession number and find out more about that gene.  But
> what I really want is to click on my actual gene models (from
> augustus or snap) and then have some functional annotation on that
> page which has been transferred onto the gene, as well as some links
> out to the appropriate external sites.  Is there a good general
> approach for doing that?
>
>
> Thanks,
> Shane
>
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