[Ergatis-users] [Gmod-help] Genome annotation tools

Wed Mar 10 13:44:17 EST 2010

Hi Dave:

Thanks for all your help! Appreciate it!

Ty

From: gmodhelp at googlemail.com [mailto:gmodhelp at googlemail.com] On Behalf Of
Dave Clements, GMOD Help Desk
Sent: Wednesday, March 10, 2010 1:16 PM
To: Ty Wang
Subject: Fwd: [Ergatis-users] [Gmod-help] Genome annotation tools

Hi Ty,

A response on the Ergatis list, which does not appear to have been sent to
you.

Dave C.

---------- Forwarded message ----------
From: Joshua Orvis <jorvis at gmail.com>
Date: 2010/3/10
Subject: Re: [Ergatis-users] [Gmod-help] Genome annotation tools
To: ergatis-users at lists.sourceforge.net

Ty -

The annotation pipeline that comes packaged with Ergatis is currently only
used for prokaryotes.  Ergatis does contain eukaryotic gene finders and
functional prediction tools, but no end-to-end automated pipeline for them
since the bulk of work on most eukaryotic projects is iterative rounds of
effort to get the structural predictions as solid as possible.  In my
experience that hasn't always lent itself to full automation.

Joshua

2010/3/10 Dave Clements, GMOD Help Desk <help at gmod.org>

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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