[ensembl-dev] Dev Digest, Vol 39, Issue 26
Joe Carl
joseph.w.carl.jr at gmail.com
Thu Sep 26 16:56:56 BST 2013
> Are you looking to view two assemblies side-by-side as in our Region
Comparison view? > Here is pig vs human:
>
http://www.ensembl.org/Sus_scrofa/Share/3c8f1202250321838e0bc96d50392e89111929907
\
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.
On Thu, Sep 26, 2013 at 7:00 AM, <dev-request at ensembl.org> wrote:
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> Today's Topics:
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> 1. Re: Adding an Alternate Assembly for a Species (Bronwen Aken)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 25 Sep 2013 16:39:55 +0100
> From: Bronwen Aken <ba1 at sanger.ac.uk>
> Subject: Re: [ensembl-dev] Adding an Alternate Assembly for a Species
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <2B0328FC-3BE5-4624-8B28-AB46067804F8 at sanger.ac.uk>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Ben,
>
> It is possible to load more than one assembly into one Ensembl database
> and we have a few examples, including:
> human (homo_sapiens_core_73_37) - four assemblies
> mouse (mus_musculus_core_73_38) - three assemblies
> dog (canis_familiaris_core_73_31) - two assemblies
> pig (sus_scrofa_core_73_102) - two assemblies
> rat (rattus_norvegicus_core_73_5) - two assemblies
>
> Are you looking to view two assemblies side-by-side as in our Region
> Comparison view? Here is pig vs human:
>
> http://www.ensembl.org/Sus_scrofa/Share/3c8f1202250321838e0bc96d50392e89111929907
>
> and here is a human assembly patch (HG79_PATCH) vs human primary assembly
> (chromosome 9):
>
> http://www.ensembl.org/Homo_sapiens/Share/ad39ce274b81b9a9247ee1095ec946ad111929907
>
>
> Below is some additional information on multiple assemblies in one
> database.
>
> Let's take pig as an example. If you look here:
> mysql -uanonymous -hensembldb.ensembl.org -P3306
> -Dsus_scrofa_core_73_102 -e "select * from coord_system"
> 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.
>
>
> The coord_system table links to the seq_region table, which gives a list
> of all the sequences and components in each assembly.
> mysql -uanonymous -hensembldb.ensembl.org -P3306
> -Dsus_scrofa_core_73_102 -e "select count(*),cs.name,cs.version from
> seq_region sr, coord_system cs where sr.coord_system_id=cs.coord_system_id
> group by cs.version,cs.name"
> +----------+------------+-------------+
> | count(*) | name | version |
> +----------+------------+-------------+
> | 186661 | contig | NULL |
> | 21 | chromosome | Sscrofa10.2 |
> | 9905 | scaffold | Sscrofa10.2 |
> | 20 | chromosome | Sscrofa9 |
> +----------+------------+-------------+
> (We don't usually give the contigs a coord_system.version because they are
> often shared between multiple assemblies.)
>
>
> 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.
>
>
> 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.
> mysql -uanonymous -hensembldb.ensembl.org -P3306
> -Dsus_scrofa_core_73_102 -e "select meta_value from meta where meta_key =
> 'assembly.mapping'"
> +---------------------------------------------+
> | meta_value |
> +---------------------------------------------+
> | chromosome:Sscrofa10.2#chromosome:Sscrofa9 |
> | chromosome:Sscrofa10.2#contig |
> | chromosome:Sscrofa10.2|scaffold:Sscrofa10.2 |
> | scaffold:Sscrofa10.2#contig |
> +---------------------------------------------+
>
> 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.)
>
> 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.
>
> Hope that helps as a start,
> Bronwen (Genebuild team)
>
>
>
> On 9 Sep 2013, at 02:18, Ben Warren <Ben.Warren at plantandfood.co.nz> wrote:
>
> > Hi,
> >
> > 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?
> >
> > i.e.
> >
> > 1. I have created an assembly of scaffolds
> > 2. I loaded that assembly into Ensembl as a new species
> > 3. I have revised the assembly, altering the scaffolds
> > 4. I would like to view the alternate assembly ?against? the
> original assembly
> >
> > Is this possible? If so is there an example of this situation in an
> existing species on ensembl.org?
> >
> >
> >
> > Thanks
> >
> > Ben Warren
> > Research Technologist
> >
> >
> >
> > F: +64 9 925 7001
> > ben.warren at plantandfood.co.nz
> > www.plantandfood.co.nz
> > The New Zealand Institute for Plant & Food Research Limited
> >
> > Postal Address: Plant & Food Research Mt Albert
> > Private Bag 92169, Auckland, 1142, New Zealand
> > Physical Address: Plant & Food Research Mt Albert
> > 120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand
> >
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