<div dir="ltr">Is there a list somewhere of all the ensembl databases and a quick description what they are used for? I've had similar questions before. <div class="gmail_extra"><br><div class="gmail_quote">On Fri, Aug 30, 2013 at 4:00 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>The multi-species database is only necessary if you are setting up an Ensembl mirror website, or if you wish to use the comparative genomics features (Compara, <a href="http://www.ensembl.org/info/docs/compara/index.html" target="_blank">http://www.ensembl.org/info/docs/compara/index.html</a>) of Ensembl.</div>
<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On 29 August 2013 18:39, Jayaraman, Pushkala <span dir="ltr"><<a href="mailto:pjayaraman@mcw.edu" target="_blank">pjayaraman@mcw.edu</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>
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<p class="MsoNormal">Hello, <u></u><u></u></p>
<p class="MsoNormal">I’m trying to install the Human variation database on our local mysql database and I was going through the instructions here:<u></u><u></u></p>
<p class="MsoNormal"><a href="http://www.ensembl.org/info/docs/webcode/install/ensembl-data.html" target="_blank">http://www.ensembl.org/info/docs/webcode/install/ensembl-data.html</a><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><b><span style="font-size:13.0pt;font-family:"Helvetica","sans-serif";color:#666666">To install the Ensembl Data:<u></u><u></u></span></b></p>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:6.0pt;margin-left:0in;line-height:12.0pt;background:white">
<u></u><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555"><span>1.<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555">Download the directory in <a href="http://ftp.ensembl.org/pub/current/mysql" target="_blank">ftp.ensembl.org/pub/current/mysql</a> for whatever organism you want to install.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:6.0pt;margin-left:0in;line-height:12.0pt;background:white">
<u></u><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555"><span>2.<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555">Each table file is gzipped so unpack the data into working directories, keeping separate directories for each database.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;line-height:15.0pt;background:white">
<span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555">For each database you have downloaded, cd into the database directory and perform steps 3-5. For illustration, we will use homo_sapiens_core_72_37 as the database - you need to
change this appropriately for each database you install. Remember, you also need to download and install the multi-species databases.<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">In this line:<u></u><u></u></p>
<p class="MsoNormal">“<span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555">Remember, you also need to download and install the multi-species databases”
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">What database is this? is there a specific database called “multi-species database” ? what does that database do? Is this absolutely necessary for the <organism>_core_72_37 or the <organism>_variation_72_37
databases to function correctly?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#555555"><u></u> <u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks,<u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">Pushkala Jayaraman<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">Programmer/Analyst - Rat Genome Database<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">Human and Molecular Genetics Center<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">Medical College of Wisconsin<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting""><a href="tel:414-955-2229" value="+14149552229" target="_blank">414-955-2229</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting""><a href="http://rgd.mcw.edu" target="_blank"><span style="color:blue">http://rgd.mcw.edu</span></a><u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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