[maker-devel] Fwd: Functional annotation of MAKER gene models

[Carson Holt]

1. yes. It should take NCBI BLAST+ results.
2. It has to be UniProt/Swissprot or you can modify the comments of another
database to look like UniProt/Swissport
3. ipr_update_gff, can also take BLAST2GO results as an undocumented feature
(or at least it could last time I tested it - which was quite a long time
ago).

Thanks,
Carson

From:  Guohong Cai <caigh02 at gmail.com>
Date:  Sunday, February 9, 2014 at 8:26 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Fwd: Functional annotation of MAKER gene models

I sent the following message to Carson but forgot to send to the maker-devel
list

Hi Carson,

Again need your help!

With your guidance, I have the gene models for my genomes. Now I am trying
to assign functions to the gene models. I noticed that I can use
maker_functional_gff/fasta or interproScan. I dig out some old messages in
maker-devel google group, but still have a few questions:

1. Will maker_functional_gff/fasta take NCBI blastp results, or only
wu-blast results? I do not have wu-blast.

2. Do I have to use Uniprot/Swiss_prot database or I can use something else?
For example, may I add a few high-quality genome annotations of related
species to the swiss_prot database? Or may I use Uniref90 or nr database
instead of swiss_prot?

3. Do you have a script to integrate blast2go results to the maker
gff/fasta?  

Thanks.

Guohong

Rutgers University 

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