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<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:#1F497D'>Hi
Dave:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:#1F497D'>Thanks
for all your help! Appreciate it!<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:#1F497D'>Ty<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmodhelp@googlemail.com
[mailto:gmodhelp@googlemail.com] <b>On Behalf Of </b>Dave Clements, GMOD Help
Desk<br>
<b>Sent:</b> Wednesday, March 10, 2010 1:16 PM<br>
<b>To:</b> Ty Wang<br>
<b>Subject:</b> Fwd: [Ergatis-users] [Gmod-help] Genome annotation tools<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Hi Ty,<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>A response on the Ergatis list, which does not appear to
have been sent to you.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal>Dave C.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'>---------- Forwarded message
----------<br>
From: <b>Joshua Orvis</b> <<a href="mailto:jorvis@gmail.com">jorvis@gmail.com</a>><br>
Date: 2010/3/10<br>
Subject: Re: [Ergatis-users] [Gmod-help] Genome annotation tools<br>
To: <a href="mailto:ergatis-users@lists.sourceforge.net">ergatis-users@lists.sourceforge.net</a><br>
<br>
<br>
Ty -<br>
<br>
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.<br>
<br>
Joshua<br>
<br>
<br>
<o:p></o:p></p>
<div>
<p class=MsoNormal>2010/3/10 Dave Clements, GMOD Help Desk <<a
href="mailto:help@gmod.org" target="_blank">help@gmod.org</a>><o:p></o:p></p>
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<p class=MsoNormal>Dear Ty,<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>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.)<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Dave C.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>On Tue, Mar 9, 2010 at 3:01 PM, Ty Wang <<a
href="mailto:tywang7@duke.edu" target="_blank">tywang7@duke.edu</a>> wrote:<o:p></o:p></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='color:black'>Dear Sir:</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='color:black'> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='color:black'>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 </span><span
style='color:#1F497D'><a href="http://www.jsbi.org/journal/GIW06/GIW06P136.pdf"
target="_blank">http://www.jsbi.org/journal/GIW06/GIW06P136.pdf</a></span><span
style='color:black'>. 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!</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='color:black'> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='color:black'>Ty</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='color:#1F497D'> </span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='color:#1F497D'> </span><o:p></o:p></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p>
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