Ensembl downtime Thur 17th May pm

Posted on May 15, 2012 by Steve Trevanion

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.

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Importing VCF files

Posted on May 14, 2012 by Will (Variation)

Variant Call Format (VCF) has become the standard portable data format for variation data. Ensembl provides various tools for handling VCF files, such as the ability to upload and view VCF data on the genome browser, and the Variant Effect Predictor (VEP) for predicting the functional consequence of variants.

We now provide an easy-to-use Perl script, import_vcf.pl, that allows you to create and populate an Ensembl Variation database from a VCF file.

Using the script you can create a database that is ready for use on your own Ensembl website mirror, as well as with Ensembl’s Perl API. Through these you have access to our powerful tools such as:

You can either build a new database from scratch, or add data on top of an existing database (for example, a copy of one of our databases downloaded from our FTP servers).

All you need is the Ensembl API modules, and a MySQL server that you can write to!

The script is located in the ensembl-variation API module, in the scripts/import/ sub-directory.

Click here for full documentation.

Posted in API and schemas, Variation | Leave a comment

Ensembl 67 has been released!

Posted on May 10, 2012 by Thomas Maurel (Production)

The latest Ensembl update (e!67) has just gone live!

This release includes one new species; Nile tilapia (Oreochromis niloticus) as well as the patches for the human assembly (GRCh37.p7) and an assembly update for two species, Pig (Sscrofa10.2) and Squirrel (SpeTri2.0).

Sequence Variation

Human structural variants from COSMIC (release 58) have been imported in Ensembl; view them in our new somatic structural variation track.  We now provide 1000 genomes phase 1 genotype data.  For other species, sequence variation for Pig, Zebrafish, Rat, Chimpanzee and Orangutan have been updated to dbSNP 136.  Variation and structural variation data are now available for Macaque (Macaca mullatta).

Patches and Haplotypes

Compare patches and haplotypes along the reference sequence for human in our newly renamed, “Region Comparison” view (previously “Multi-species view”) on the browser.  Jump there from a patch or haplotype region on Region in Detail, as in the image.

New Species

The Nile tilapia (Orenil1.0) assembly was provided by the Broad Institute. Illumina technology was used to produced this high quality draft. A mixed approach was used for the genebuild using the RNA-Seq pipeline and the Ensembl pipeline.

Virtual Machine

In other exciting news, Ensembl now has a virtual machine with all the Ensembl APIs and the VEP (Variant Effect Predictor) pre-installed  and ready to use. Just make sure you have virtualization software on your machine, download the Ensembl pre-configured file and install it. Detailed information can be found in the Ensembl Tools section.

More news is available on the Ensembl website.

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Retirement of archive 53 (March 2009)

Posted on May 4, 2012 by Ensembl

Please note that the archive website for Ensembl release 53 (March 2009) will be retired next week when version 67 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). Since zebrafish is currently on assembly Zv9, the e53 archive (which contains the last instance of Zv7) is not being retained under these rules; however the Zv7 assembly will be available on archive 46 until a new version of the mouse assembly is released this summer.

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.

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New Pre! sites for Painted turtle and Spotted gar

Posted on April 24, 2012 by Bronwen (Genebuild)

Pre! sites have been released for two species: Western painted turtle (Chrysemys picta bellii) and Spotted gar (Lepisosteus oculatus).

Chrysemys picta bellii

The western painted turtle assembly Chrysemys_picta_bellii-3.0.1 (GCA_000241765.1) was submitted by the International Painted Turtle Genome Sequencing Consortium. The painted turtle is used as a model species for studying anoxia tolerance, freeze tolerance, temperature-dependent sex determination, and vertebrate evolution. This assembly is composed of 80983 unplaced scaffolds. Click here to go to the painted turtle Pre! site where you can view transcripts built from alignments of a few painted turtle proteins (from UniProtKB) as well as from alignments of chicken and green anole lizard translations (from Ensembl release 66).

Lepisosteus oculatus

The spotted gar assembly LepOcu1 (GCA_000242695.1) was submitted by the Broad Institute. The spotted gar is a primitive freshwater fish. It is especially interesting as an outgroup to teleost fishes: the gar lineage diverged from teleosts before the teleost whole-genome duplication. This assembly is composed of 29 chromosomes and 1896 unplaced scaffolds. Click here to go to the spotted gar Pre! site where you can view alignments of zebrafish, stickleback and coelacanth translations from Ensembl release 67.

Posted in Assembly & Genebuild | Leave a comment

Ensembl Down South

Posted on April 17, 2012 by Giulietta (Outreach)

Ensembl is in Uruguay!  We’re teaching a workshop alongside instructors from VEGA/HAVANA, Janelia Farm Research Campus, Duke University Center for Human Genetics, and University of Maryland.  The Open Door Workshop is funded by the Wellcome Trust, and provides different bioinformatics tools to analyse the human genome.  At our workshop this week, we have professors and researchers from nine different countries in South and Central America.

Our training manual is on the Open Door Workshop page, so go ahead and check it out if you want to know more.  And remember, if you would like to host an Ensembl browser workshop at your institute, contact us!

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Upcoming conferences: Posters on Ensembl Gene Annotation

Posted on April 2, 2012 by Giulietta (Outreach)

If you’re at the Biocuration conference currently happening in Washington DC, feel free to swing by the poster of Amonida Zadissa to learn about the Ensembl gene set (poster number P.87).

Ensembl Genebuild members will also be attending:

5th International Conference on Primate Genomics Bronwen Aken
17-19 April 2012
Houston, Texas, USA

Recomb 2012  Thibaut Hourlier, Poster 276
First session, 21st April, 18:30-20:00
Conference on Research in Computational Molecular Biology
21-24 April 2012
Barcelona, Spain

 

 

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Archive Sites

Posted on March 29, 2012 by Giulietta (Outreach)

Ensembl archive sites allow you to browse older versions of our website (and the underlying data).  These are maintained going back three years from the live version.

Versions 50-52 of the website (2008) will be retired tomorrow (30 March).   Data and code for these releases are still available using MySQL or the Perl API.  No major genome assembly changes are included in these versions.

Archives are especially useful in citing our webpages in publications.  As Ensembl has frequent updates (every two months) it is useful to use the ‘permalink’ found at the bottom left of Ensembl views.

 

The url will follow the format of this example:

http://Feb2012.archive.ensembl.org

and will bring the reader to that specific Ensembl version, rather than the live site (at www.ensembl.org).

Cheers,

The Ensembl Team

 

 

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New Pre! sites for platyfish, budgerigar

Posted on March 13, 2012 by Rishi (Genebuild)

Pre! sites have been released for two species: Southern Platyfish (Xiphophorus maculatus) and Budgerigar (Melopsittacus undulatus).

Xiphophorus maculatus

The playtfish assembly Xiphophorus maculatus 4.4.2 (GCA_000241075.1) was submitted by the The Genome Institute, Washington University at St. Louis. The Southern Platyfish is of interest for development of malignant melanoma when crossed with other members of the Xiphophorus family, and the family is used as a model for the study of hereditary cancer. This assembly is composed of 20,640 unplaced scaffolds. Click here to go to the platyfish Pre! site, where you can view platyfish protein and EST alignments, as well as alignments of the Ensembl release 65 zebrafish and stickleback translations. This assembly will undergo full automatic gene annotation in due course.

 

Melopsittacus undulatus

The budgerigar assembly Melopsittacus_undulatus_6.3 (GCA_000238935.1) was submitted by the The Genome Institute, Washington University at St. Louis. The budgerigar is important as a model species in the study of hereditary mutations which cause color variation in the feathers. This assembly is composed of 25211 unplaced scaffolds. Click here to go to the budgerigar Pre! site, where you can view budgerigar protein alignments, as well as alignments of the Ensembl release 65 human, chicken and zebra finch translations. This assembly will undergo full automatic gene annotation in due course.

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Ensembl Genomes release 13

Posted on March 8, 2012 by Denise (Outreach)

The Ensembl Genomes Project is pleased to announce release 13 of Ensembl Genomes.

This release contains 6 new genomes, bringing the total genomes supported to 341. Main highlights are:

* Software migration to Ensembl 66

* The addition of Brassica rapa to Ensembl Plants, as well as synteny data for species in the Arabidopsis and Oryza genomes and new oligo probe mapping from the GeneChip Maize Genome Array for Zea mays

* A new species (Toxoplasma gondii ME49) added to Ensembl Protists and the genome of Trichinella spiralis is now available in Ensembl Metazoa.

* Three new genomes in Ensembl Fungi: Magnaporthe oryzae, Magnaporthe poae and Gaeumannomyces graminis. There is also synteny data for species in the Saccharomycetales and Hypocrealestaxonomy groups. The annotation for S. pombe has been updated to reflect the most recent content from PomBase.

* EMBL-EBI and Rothamsted Research have recently announced the release of the PhytoPath portal, a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection.  Genomes of pathogenic organisms from this project including the causative agents of diseases such as potato blight, rice blast and wheat rust can be found in this release of Ensembl Genomes.

The Ensembl Genomes Team

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