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Hi Denise
<div>I appreciate your help. I have the same sort of problem as Joe. I can bring up the gene but it never looks as good as the displays you guys show. Maybe its secreta of configuring the display. Can you dump your configuration so we can match it?</div>
<div><br>
</div>
<div>Thanks </div>
<div>Ed</div>
<br>
<br>
<br>
-------- Original message --------<br>
From: Denise Carvalho-Silva <denise@ebi.ac.uk> <br>
Date: 09/26/2013 12:23 PM (GMT-05:00) <br>
To: Ensembl developers list <dev@ensembl.org> <br>
Subject: Re: [ensembl-dev] Dev Digest, Vol 39, Issue 26 <br>
<br>
<br>
<div style="word-wrap:break-word">Hi Joe,
<div><br>
</div>
<div>From this link you sent us, you can simply type in VWF in the Gene box and the page will automatically reload on the region where the porcine VWF is annotated.</div>
<div><br>
</div>
<div><img height="545" width="851" id="x_7438c837-386a-48e6-90a2-2b26b4f9659b" src="cid:529490CF-D9B4-4E9B-88FD-7894F0C6FD40@windows.ebi.ac.uk"><br>
<div>
<div><br>
</div>
<div>This is what you should see:</div>
<div><br>
</div>
<div><a href="http://www.ensembl.org/Sus_scrofa/Share/860487e6b4a640afe589cad3ede5422c114167076">http://www.ensembl.org/Sus_scrofa/Share/860487e6b4a640afe589cad3ede5422c114167076</a></div>
<div><br>
</div>
<div>You can zoom in and out as you wish.</div>
<div><br>
</div>
<div>More details on this view can be found here:</div>
<div><br>
</div>
<div><a href="http://www.ensembl.org/Help/View?id=225">http://www.ensembl.org/Help/View?id=225</a></div>
<div><br>
</div>
<div>Hope it helps.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Denise</div>
<div><br>
</div>
<div>On 26 Sep 2013, at 16:56, Joe Carl wrote:</div>
<br class="x_Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr"><span style="font-family:arial,sans-serif; font-size:13px">> Are you looking to view two assemblies side-by-side as in our Region Comparison view? > Here is pig vs human:</span><br style="font-family:arial,sans-serif; font-size:13px">
<span style="font-family:arial,sans-serif; font-size:13px">> </span><a href="http://www.ensembl.org/Sus_scrofa/Share/3c8f1202250321838e0bc96d50392e89111929907" target="_blank" style="font-family:arial,sans-serif; font-size:13px">http://www.ensembl.org/Sus_scrofa/Share/3c8f1202250321838e0bc96d50392e89111929907</a>\<br>
<div><br>
</div>
<div><br>
</div>
<div>I would love to know how to do this with a protein like VWF. What is the general way to view a Pig gene next to a human gene in this kind of browser view? I can't seem to figure it out.</div>
</div>
<div class="x_gmail_extra"><br>
<br>
<div class="x_gmail_quote">On Thu, Sep 26, 2013 at 7:00 AM, <span dir="ltr"><<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a>></span> wrote:<br>
<blockquote class="x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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Today's Topics:<br>
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1. Re: Adding an Alternate Assembly for a Species (Bronwen Aken)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 25 Sep 2013 16:39:55 +0100<br>
From: Bronwen Aken <<a href="mailto:ba1@sanger.ac.uk">ba1@sanger.ac.uk</a>><br>
Subject: Re: [ensembl-dev] Adding an Alternate Assembly for a Species<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:2B0328FC-3BE5-4624-8B28-AB46067804F8@sanger.ac.uk">2B0328FC-3BE5-4624-8B28-AB46067804F8@sanger.ac.uk</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hi Ben,<br>
<br>
It is possible to load more than one assembly into one Ensembl database and we have a few examples, including:<br>
human (homo_sapiens_core_73_37) - four assemblies<br>
mouse (mus_musculus_core_73_38) - three assemblies<br>
dog (canis_familiaris_core_73_31) - two assemblies<br>
pig (sus_scrofa_core_73_102) - two assemblies<br>
rat (rattus_norvegicus_core_73_5) - two assemblies<br>
<br>
Are you looking to view two assemblies side-by-side as in our Region Comparison view? Here is pig vs human:<br>
<a href="http://www.ensembl.org/Sus_scrofa/Share/3c8f1202250321838e0bc96d50392e89111929907" target="_blank">
http://www.ensembl.org/Sus_scrofa/Share/3c8f1202250321838e0bc96d50392e89111929907</a><br>
<br>
and here is a human assembly patch (HG79_PATCH) vs human primary assembly (chromosome 9):<br>
<a href="http://www.ensembl.org/Homo_sapiens/Share/ad39ce274b81b9a9247ee1095ec946ad111929907" target="_blank">http://www.ensembl.org/Homo_sapiens/Share/ad39ce274b81b9a9247ee1095ec946ad111929907</a><br>
<br>
<br>
Below is some additional information on multiple assemblies in one database.<br>
<br>
Let's take pig as an example. If you look here:<br>
mysql -uanonymous -<a href="http://hensembldb.ensembl.org/" target="_blank">hensembldb.ensembl.org</a> -P3306 -Dsus_scrofa_core_73_102 -e "select * from coord_system"<br>
you will see that we have two different coordinate system versions: Sscrofa9 and Sscrofa10.2. Each of these coordinate system versions represents a different assembly.<br>
<br>
<br>
The coord_system table links to the seq_region table, which gives a list of all the sequences and components in each assembly.<br>
mysql -uanonymous -<a href="http://hensembldb.ensembl.org/" target="_blank">hensembldb.ensembl.org</a> -P3306 -Dsus_scrofa_core_73_102 -e "select count(*),<a href="http://cs.name/" target="_blank">cs.name</a>,cs.version from seq_region sr, coord_system cs
where sr.coord_system_id=cs.coord_system_id group by cs.version,<a href="http://cs.name/" target="_blank">cs.name</a>"<br>
+----------+------------+-------------+<br>
| count(*) | name | version |<br>
+----------+------------+-------------+<br>
| 186661 | contig | NULL |<br>
| 21 | chromosome | Sscrofa10.2 |<br>
| 9905 | scaffold | Sscrofa10.2 |<br>
| 20 | chromosome | Sscrofa9 |<br>
+----------+------------+-------------+<br>
(We don't usually give the contigs a coord_system.version because they are often shared between multiple assemblies.)<br>
<br>
<br>
It sounds like your assemblies have only one coord_system, scaffolds, whereas pig's Sscrofa9 has contigs and chromosomes and pig's Sscrofa10.2 assembly has contigs, scaffolds and chromosomes. The links between contigs, scaffolds and chromosomes are stored
in the assembly table.<br>
<br>
<br>
We also store which parts of the assemblies 'map' to one another. Within one assembly, the mapping between its contigs, scaffolds and chromosomes are provided in an "AGP" file given with the assembly. The chromosome-to-chromosome mapping (top line in the query
below) was an additional step added by our Core team to link the two assemblies. We (Ensembl Core team) will be able to give you more information on how to do that.<br>
mysql -uanonymous -<a href="http://hensembldb.ensembl.org/" target="_blank">hensembldb.ensembl.org</a> -P3306 -Dsus_scrofa_core_73_102 -e "select meta_value from meta where meta_key = 'assembly.mapping'"<br>
+---------------------------------------------+<br>
| meta_value |<br>
+---------------------------------------------+<br>
| chromosome:Sscrofa10.2#chromosome:Sscrofa9 |<br>
| chromosome:Sscrofa10.2#contig |<br>
| chromosome:Sscrofa10.2|scaffold:Sscrofa10.2 |<br>
| scaffold:Sscrofa10.2#contig |<br>
+---------------------------------------------+<br>
<br>
In order to load your two assemblies into one database, you'd need to set them with two different coord_system.version values. (Alternately, you could just load one assembly each into two databases.)<br>
<br>
If the next step you're after is to view these two assemblies side-by-side, as in our Region Comparison view, additional information is required. Our Compara team usually align the two assemblies (LASTZ) and store the information in our 'compara' schema database.
This information is used by the web code to generate the Region Comparison view. If you already know the scaffold-to-scaffold mapping for your two assemblies then I don't think you'd need to do the LASTZ alignment but I do think you'd need to still store the
links in a compara-schema database. We (Ensembl Compara team) can help with that too.<br>
<br>
Hope that helps as a start,<br>
Bronwen (Genebuild team)<br>
<br>
<br>
<br>
On 9 Sep 2013, at 02:18, Ben Warren <<a href="mailto:Ben.Warren@plantandfood.co.nz">Ben.Warren@plantandfood.co.nz</a>> wrote:<br>
<br>
> Hi,<br>
><br>
> I am running a local Ensembl instance using species data stored in a local database. Is it possible to add an additional ?alternate? assembly to an Ensembl species?<br>
><br>
> i.e.<br>
><br>
> 1. I have created an assembly of scaffolds<br>
> 2. I loaded that assembly into Ensembl as a new species<br>
> 3. I have revised the assembly, altering the scaffolds<br>
> 4. I would like to view the alternate assembly ?against? the original assembly<br>
><br>
> Is this possible? If so is there an example of this situation in an existing species on
<a href="http://ensembl.org/" target="_blank">ensembl.org</a>?<br>
><br>
><br>
><br>
> Thanks<br>
><br>
> Ben Warren<br>
> Research Technologist<br>
><br>
><br>
><br>
> F: <a href="tel:%2B64%209%20925%207001" value="+6499257001">+64 9 925 7001</a><br>
> <a href="mailto:ben.warren@plantandfood.co.nz">ben.warren@plantandfood.co.nz</a><br>
> <a href="http://www.plantandfood.co.nz/" target="_blank">www.plantandfood.co.nz</a><br>
> The New Zealand Institute for Plant & Food Research Limited<br>
><br>
> Postal Address: Plant & Food Research Mt Albert<br>
> Private Bag 92169, Auckland, 1142, New Zealand<br>
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