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

[Dave Clements, GMOD Help Desk]

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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