In line with EMBL-EBI policy, from the end of 2015 Ensembl will be removing support for DAS from our browser. This means that we will no longer provide our annotations over DAS and that we will not visualise third party annotation provided to us via DAS. If you have data with genomic coordinates that you wish to present in Ensembl then we recommend that you do this using TrackHubs. For annotation on other coordinate systems, we are currently working on providing support for this and will announce developments in this area over the course of the coming year. If you need more details then please get in touch with us at helpdesk@ensembl.org.

We’re pleased to announce that Ensembl now provides a public MySQL server hosted in Singapore – asiadb.ensembl.org. For users in that part of the world this should be much faster to query than the main server (ensembldb.ensembl.org) which is based in the UK. The new mirror server is similar to our US based mirror in that it contains databases for the two latest releases of Ensembl only; if you require access to earlier data you will need to continue to use ensembldb.ensembl.org. Please see the Ensembl website for connection details.

Please note that the archive website for Ensembl release 65 (Dec 2011) will be retired in December when version 78 is released.

This is in accordance with our rolling retirement policy, whereby archives more than three years old are retired unless they include the last instance of the previous assembly from one of our key species (human, mouse and zebrafish).

For more information about how to use archives, please see our previous blog post on the topic; a list of all current archives is available on the main website.

Please note that the archive websites for Ensembl release 62 (April 2011) and 63 (June 2011) will be retired in August when version 76 is released.

This is in accordance with our rolling retirement policy, whereby archives more than three years old are retired unless they include the last instance of the previous assembly from one of our key species (human, mouse and zebrafish).

For more information about how to use archives, please see our previous blog post on the topic; a list of all current archives is available on the main website.

We are pleased to announce the public release of manual annotation on the new human GRCh38 assembly on the Vega website.This release follows on from the publication of a preliminary gene set on Pre! Ensembl and represents one of the final steps before the release of the full human Gencode 20 gene set in Ensembl release 76.

Vega website.

The Vega website uses Ensembl technology to present the latest manual annotation produced by the Havana group based at the Welcome Trust Sanger Institute. It has significance for researchers who want to see the most up to date annotation – every two weeks we run a streamlined, automated production pipeline that identifies new or updated annotation and presents it on Vega. Consequently there is never more than 14 days between annotation being created or updated by Havana and being made available to the public.

Vega update gene

Annotation of gene PCDHB9 has been updated within the last two weeks

Human GRCh38 manual annotation gene set.

The actual gene numbers have not changed greatly overall, but there has been a lot of work going on in the background to refine the gene set. The numbers of genes on GRC patches have been reduced from GRCh37 as many of these patches have now been incorporated into the primary genome assembly.

The initial step in the manual annotation of the new assembly was a computational one, projecting the manual annotation from GRCh37 onto GRCh38. As a part of this process we generated a list of the loci that did not project due to genomic changes. Many of them were in the regions of greatest change between assemblies including regions of chromosomes 1, 9, 17 and X. There were about 800 of these loci, and each of these needed manual intervention. This took a dedicated effort by the Havana group over about a three week period. The changes made fall into a number of categories:

(i) The use of single haplotypes across certain gene clusters, such as the XAGE and GAGE gene families on the X chromosome.

(ii) Filling, moving or even introducing gaps in the assembly to give a much more accurate representation of difficult regions. An example of such re-arrangement is the XAGE1B gene that is now placed on the opposite strand compared to the previous assembly.

(iii) A decrease in the number of polymorphic pseudogenes due to changes made in the assembly to include a haplotype with a coding version of the gene.  Polymorphic pseudogenes are coding in some individuals and disabled in other individuals due to sequence variation.

(iv) A large increase in the number of long non-coding RNAs (lncRNA) because we have been able to take advantage of new RNA-seq and PolyA-seq data rather than because of the new assembly per se.

Further annotation of the new assembly is ongoing, with the focus having changed from fixing projection errors to finalizing the annotation.

Merge with Ensembl geneset (Gencode 20)

The Havana manual annotation has been merged with the annotation arising from the rerun of the Ensembl genebuild pipeline. This improves the gene set, primarily by taking into account new experimental evidence generated since the manual annotation was originally performed. In addition, the comparison between the manually and automatically generated gene sets contributes to the continuous enhancement of both annotation systems. It is the merged gene set that will be released as Gencode 20.

All Sanger located Ensembl based websites (www.ensembl.org, pre.ensembl.org, archives and vega.sanger.ac.uk) will be unavailable for a short period on Mon, 16th July from 1300 GMT. We expect the maintenance to be completed within the hour.

Ensembl mirrors (useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org) will continue to operate, but note that user logins from these will not be available during this period.

Apologies for the inconvenience this may cause.

BLAST and BLAT will be unavailable for a short period from 13.00 BST on Wed 20th June due to some hardware maintenance being required. We expect this work to be complete within the hour. This will affect the main Ensembl site and the mirror sites.

BLAST and BLAT will be unavailable for a short period from 13.00 BST on Thur 24th due to some hardware maintenance being required. We expect this work to be complete within the hour.
This will affect the main Ensembl site, mirror sites, Vega and Pre Ensembl.

Apologies for any inconvenience caused,

Regards,

Steve

Due to urgent maintenance being required, all Sanger located Ensembl based websites (www.ensembl.org, pre.ensembl.org, archives and vega.sanger.ac.uk) will be unavailable for a short period on Thur, 17th May from 1300 GMT. We expect the work to be completed within the hour.

Ensembl mirrors (useast.ensembl.org, uswest.ensembl.org and asia.ensembl.org) will continue to operate, but note that user logins from these will not be available during this period.

Apologies for the inconvenience this may cause.

The Sanger BLAST servers are scheduled for maintenance on the afternoon of Sunday 22nd May. The queues will therefore be closed to new queries from around 1pm on the Sunday, and access from Ensembl to BLAST will be disabled during this time. This will affect the main Ensembl site and all mirrors.

Please accept our apologies for any inconvenience caused.