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

[Guohong Cai]

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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