[ensembl-dev] Ensembl Genomes release announcement

Fri Feb 15 13:41:40 GMT 2013

Hello Sunita,

Ensembl is based on the patch 10 release:

http://www.ensembl.org/Homo_sapiens/Info/Annotation/#assembly

Note though that the fix patches are not incorporated in the primary
assembly (this will be done when we move to GRCh38), but we do have
annotated the patches, so for genes in these regions you will find two
gene models, one annotated on the primary assembly and one annotated
on the fix patch.

Hope this helps.

Cheers,
Bert

On Fri, Feb 15, 2013 at 1:38 PM, Koul, Sunita
<sunita at pathology.wustl.edu> wrote:
> Thanks Bert
> I wanted to check which minor release of hg19 is  the annotation based on.
> The latest release I believe is hg19.11
>
> Thanks
> Sunita
>
> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Bert Overduin
> Sent: Friday, February 15, 2013 7:32 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Ensembl Genomes release announcement
>
> Hello Sunita,
>
> Human is part of Ensembl (which contains the genomes of vertebrates), not Ensembl Genomes (which contains the genomes of invertebrates, plants, fungi, protists and bacteria).
>
> Currently the annotation for human in Ensembl is based on the GRCh37 assembly (or in UCSC speak "hg19").
>
> Hope this helps.
>
> Cheers,
> Bert
>
> On Fri, Feb 15, 2013 at 1:29 PM, Koul, Sunita <sunita at pathology.wustl.edu> wrote:
>> For Human genome which version of NCBI is this version comparable to
>>
>> THanks
>> Sunita
>>
>> -----Original Message-----
>> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On
>> Behalf Of denise at ebi.ac.uk
>> Sent: Thursday, February 07, 2013 2:54 PM
>> To: dev at ensembl.org
>> Subject: [ensembl-dev] Ensembl Genomes release announcement
>>
>> Dear all,
>>
>> The Ensembl Genomes project is pleased to announce release 17 of Ensembl Genomes.
>>
>> Our latest release brings over 6,000 bacterial genomes into Ensembl for the first time ever! Users can browse these data interactively on the web with our graphical interface. Programmatic access is available through the Perl and RESTful Ensembl APIs, and through publicly accessible mysql databases. Full data dumps such as DNA sequence and protein sequence in FASTA format, annotations in GTF format, and mysql dump files are also provided on our FTP sites.
>>
>> Due to this sheer number of new genomes in Ensembl Bacteria in release 17, BioMart access is no longer possible and we are now working on alternative and more powerful data retrieval tools.
>>
>> An increased number of bacteria (over 120 genomes) has now been used for comparative genomics analyses across a wider range of non-bacterial genomes (from both Ensembl and Ensembl Genomes projects). This is known as Pan-taxonomic Compara and can be visualised in the gene views on the browser or accessed through the Compara database.
>>
>> In addition to the thousands of new bacterial genomes, we also have six new genomes in Ensembl Fungi and one new genome in Ensembl Protists. We have also improved existing genomes and added new variation, comparative genomics and transcriptomics data for several species.
>>
>> The significant milestones of this release are:
>>
>> Ensembl Bacteria:
>> * Protein families are now classified based on PANTHER and HAMAP matches.
>> Gene trees are provided for several but not for all bacterial genomes
>>
>> * Pan-taxonomic compara now contains 123 key bacterial genomes
>>
>> * Gene families are now populated by dividing all proteins on all
>> genomes by HAMAP and PANTHER classification provided by InterPro
>>
>> Ensembl Fungi:
>> * Six new genomes: Komagataella pastoris, Sporisorium reilianum,
>> Pyrenophora teres, Pyrenophora tritici-repentis, Glomerella
>> graminicola and Melampsora larici-populina
>>
>> * New EST alignments for Melampsora larici-populina, Glomerella
>> graminicola and Leptosphaeria maculans
>>
>> * Mycosphaerella graminicola has been renamed to Zymoseptoria tritici
>>
>> Ensembl Metazoa:
>> * Updated gene sets for Anopheles gambiae
>>
>> * Updated gene sets for Drosophila pseudoobscura (FlyBase version
>> 2.30) and Drosophila simulans (FlyBase version 1.4)
>>
>> * Updated cross-references for all 12 drosophilid species
>>
>> * A missing chromosome in beetle (Tribolium castaneum) was also
>> reinstated, and its gene models updated
>>
>> Ensembl Plants:
>> * New and extensive variation dataset for Hordeum vulgare (barley)
>>
>> * Triticum aestivum (wheat) EST and RNA-seq alignments in the syntenic
>> context of Brachypodium are now available
>>
>> * New wheat sequence search facility based on extensive genomic and
>> transcriptomic data aligned to Brachypodium
>>
>> * Solanum tuberosum (potato) EST and RNA-seq alignments are also now
>> available
>>
>> * New pairwise alignments between several plant genomes.
>>
>> Ensembl Protists:
>> * A new genome of a flagellated protozoan parasite, Giardia lamblia,
>> is now available
>>
>> Software migration to Ensembl 70
>>
>> Have fun!
>>
>> The Ensembl Genomes Team
>>
>>
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>
>
>
> --
> Bert Overduin, Ph.D.
> Vertebrate Genomics Team
>
> EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom
>
> http://www.ebi.ac.uk/~bert
>
> Ensembl browser: http://www.ensembl.org
>
> Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html
>
> Blog: http://www.ensembl.info
>
> YouTube: http://www.youtube.com/user/EnsemblHelpdesk
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>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
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>
> _______________________________________________
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> Ensembl Blog: http://www.ensembl.info/

-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert

Ensembl browser: http://www.ensembl.org

Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html

Blog: http://www.ensembl.info

YouTube: http://www.youtube.com/user/EnsemblHelpdesk
Facebook: http://www.facebook.com/Ensembl.org
Twitter: http://twitter.com/Ensembl