<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>I would agree blast2go.</div><div><br></div><div>You can also try interproscan fro the EBI</div><div><br></div><div>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.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Joseph Fass <<a href="mailto:joseph.fass@gmail.com">joseph.fass@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Fri, 13 Apr 2012 13:42:51 -0700<br><span style="font-weight:bold">To: </span> Shane Brubaker <<a href="mailto:sbrubaker@solazyme.com">sbrubaker@solazyme.com</a>><br><span style="font-weight:bold">Cc: </span> "<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><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Functional annotation pipeline<br></div><div><br></div>Would <a href="http://blast2go.de/b2ghome">http://blast2go.de/b2ghome</a> be the kind of thing you're looking for?<div>HTH,</div><div>~Joe</div><div><br><div class="gmail_quote">On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <span dir="ltr"><<a href="mailto:sbrubaker@solazyme.com">sbrubaker@solazyme.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
_______________________________________________<br>
maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Joseph Fass<br>Lead Data Analyst<div>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)</div><br></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>