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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Great thank you … I will take a look at those.<o:p></o:p></span></p>
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<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""> Carson Holt [mailto:carsonhh@gmail.com]
<br>
<b>Sent:</b> Friday, April 13, 2012 2:03 PM<br>
<b>To:</b> Joseph Fass; Shane Brubaker<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] Functional annotation pipeline<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">I would agree blast2go.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">You can also try interproscan fro the EBI<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help integrate interproscan results in the GFF3 files. There are also a couple of scripts maker_functional_gff
and maker_functional_fasta that can do putative functional annotation using uniprot/swiss-prot.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Thanks,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Carson<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">From:
</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Joseph Fass <<a href="mailto:joseph.fass@gmail.com">joseph.fass@gmail.com</a>><br>
<b>Date: </b>Fri, 13 Apr 2012 13:42:51 -0700<br>
<b>To: </b>Shane Brubaker <<a href="mailto:sbrubaker@solazyme.com">sbrubaker@solazyme.com</a>><br>
<b>Cc: </b>"<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<b>Subject: </b>Re: [maker-devel] Functional annotation pipeline<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Would <a href="http://blast2go.de/b2ghome">http://blast2go.de/b2ghome</a> be the kind of thing you're looking for?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">HTH,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">~Joe<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <<a href="mailto:sbrubaker@solazyme.com">sbrubaker@solazyme.com</a>> wrote:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?<br>
<br>
Thanks,<br>
Shane<br>
<br>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">--
<br>
Joseph Fass<br>
Lead Data Analyst<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri","sans-serif";color:black">UC Davis Bioinformatics Core<br>
joseph.fass -at- <a href="http://gmail.com" target="_blank">gmail.com</a> (professional)<br>
970.227.5928 (c) || 530.752.2698 (w)<o:p></o:p></span></p>
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