Careful of interproscan atm.. I believe the executable is still in beta and they definitely aren't recommending it for production use yet. If you do use it be sure to check output file if using the lookup service as when i used it recently it would sometimes exit normally despite lookup failures (the lookup problems may have had something to do with running ~800 in parallel - they're looking into the issue atm.).<br>
<br>dan.<br><br><br clear="all">Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)<br>-------------------------------------------------------------------------------------<br><a href="mailto:dsth@cantab.net">dsth@cantab.net</a><br>
<a href="mailto:dsth@cpan.org">dsth@cpan.org</a><br>
<br><br><div class="gmail_quote">2012/4/13 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><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><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Joseph Fass <<a href="mailto:joseph.fass@gmail.com" target="_blank">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" target="_blank">sbrubaker@solazyme.com</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">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" target="_blank">http://blast2go.de/b2ghome</a> be the kind of thing you're looking for?<div>
HTH,</div><div>~Joe</div><div><div><div class="h5"><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" target="_blank">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>
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</blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <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>
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