[maker-devel] [Gmod-help] Genome annotation tools

[Carson Holt]

Yes, you can use MAKER for the structural annotations, and MAKER is compatible with MPICH2.  MAKER also comes with some accessory scripts that assist in adding functional annotations directly to the GFF3 file using InterProScan.  These accessory scripts add InterPro protein domains and GO function categories to each gene model in the GFF3 file automatically.  There is also a simple accessory script that adds putative overall gene function descriptions based on similarity to UniProt/SwissProt genes.

Thanks,
Carson


On 3/10/10 10:47 AM, "Dave Clements, GMOD Help Desk" <help at gmod.org> wrote:

Dear Ty,

I've forwarded your query on to the MAKER and Ergatis mailing lists.  The MAKER team can address your question about functional annotation.  Ergatis is a workflow management system that is also part of GMOD.  If you have a compute cluster and other types of pipelines to run then you may want to look at that as well.  (MAKER can also take advantage of a compute cluster.)

Dave C.

On Tue, Mar 9, 2010 at 3:01 PM, Ty Wang <tywang7 at duke.edu> wrote:
Dear Sir:

How are you? I am a bioinformatician working at Duke Sequencing Core facility. I work on a lichen genome annotation project. Lichen has two genomes, mycobiont and photobiont. We are looking for tools software for automated genome annotation in non-model systems. So far, we are interested in two software packages specifically (but open to any suggestion). One of them is called MAKER recommended by GMOD. The other one is JGI annotation pipeline http://www.jsbi.org/journal/GIW06/GIW06P136.pdf. MARKER is good at gene structural annotation. And JGI annotation pipeline provides additional functional annotation. I could be wrong. What do you think? This is my first time working on a genome annotation projection. I would really appreciate if you can give me any suggestion or direct me to the right person. Looking forward to your reply. Thanks!

Ty






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