The Ensembl project is pleased to announce release 60 of Ensembl. Highlights of this release are:

* New species – Giant Panda
* New assemblies and genebuilds for zebrafish and rabbit
* Improved design of the Variation Table
* New display for GO terms
* Improved navigation on Region in Detail, including autocompletion of gene display names (e.g. HGNC)

For more information visit:
http://e60.ensembl.org/info/website/news/index.html

The Ensembl Team

The Ensembl Genomes Project is pleased to announce release 6 of Ensembl Genomes.

The highlights of this release are:

  • Software migration to Ensembl 59.
  • Two new rodent malarial genomes: Plasmodium berghei and Plasmodium chabaudi and an update to the Plasmodium falciparum gene-set in Ensembl Protists.
  • Variation BioMarts added for Plasmodium falciparum, Saccharomyces cerevisiae (Ensembl Fungi), Arabidopsis thaliana, Oryza sativa indica, Oryza sativa japonica, Vitis vinifera (Ensembl Plants), Anopheles gambiae and Drosophila melanogaster (Ensembl Metazoa).

See the individual homepages for Bacteria, Protists, Fungi, Plants and Metazoa for more information.

With the recent release of version 58, we are pleased to announce a few features designed to make genome browsing simpler. Have you noticed the search function in the individual tables? For example, in the Gene tab: “Variation Table“, search for a variation ID.

Have a look at our sortable tables. In this example, we can sort by ID, Type, location, allele, source, or validation status. Use the arrows next to the column title to choose a new column to sort by. Searchable, and sortable, tables can also be found for orthologues, variations across individuals or strains, protein motifs and domains, and more.

If you are browsing a genomic region, you may have noticed that the Location tab: “Region in detail” view has a sliding zoom bar. Zoom out to view neighbouring genes and features, or zoom in to your favourite exon.

We have been developing a pipeline to build gene models using only RNA-seq data. For release 58 we have added a preliminary set of Zebrafish RNA-seq gene models with an intention to integrate this new source of evidence into a full genebuild soon.

Zebrafish transcriptome data from 9 tissues were used to build a set of genes and splice variants. For each loci we chose the variant with the highest read support to display, further details on the process are available here.
To display the genes, go to the Region in Detail, or Region Overview. Use the “Configure this page” button and select “RNASeq Genes” from the “Genes” menu. The “Supporting DNA Alignments” menu contains supporting exon and intron features from each of the nine tissues. Clicking on these features in Ensembl location pages shows a simple read count for the intron features and RPKM values for transcripts and exons, (reads per kilobase of model per million mapped reads, from Mortazavi Nature Methods 2008).

This is a first attempt at visualising tissue specific read depth and alternative splicing, which we hope to develop further in the future.

The Ensembl Genomes Project is pleased to announce release 5 of Ensembl Genomes.

The main highlights of this release are:

  • Software migration to Ensembl 58
  • Total of 6 new bacterial genomes for Escherichia/Shigella and Staphylococcus collections for Ensembl Bacteria; pairwise alignments added for all collections.

  • 2 new genomes, Phaeodactylum tricornutum and Thalassiosira pseudonana, for Ensembl Protists; pairwise alignments added.

  • Pristionchus pacificus genome from Wormbase and updates to the Drosophilia variation database added to Ensembl Metazoa.

  • Updates to the variation databases for A.thaliana, O.sativa japonica and V.vinifera in Ensembl Plants.

For further details regarding this release please visit:
http://ensemblgenomes.org/releases/release5_notes


We are pleased to announce the fourth release of Ensembl Genomes.

Ensembl Genomes is a companion project to Ensembl designed to provide access to genome scale data for non-chordate species of scientific interest.

Features of the new release include the addition of new databases for the bread mould Neurospora crassa to the Ensembl Fungi division, the slime mould Dictyostelium discoideum (built with the assistance of dictyBase) to Ensembl Protists, and the body louse Pediculus humanus (containing data provided by VectorBase) to Ensembl Metazoa.

The release also includes new variation databases for Drosophila melanogaster (using data from the Drosophila Population Genomics Project) and Plasmodium falciparum; the update of existing variation databases for Arabidopsis thaliana and Vitis vinifera in Ensembl Plants; and the addition of three new clades to Ensembl Bacteria.

Ensembl Genomes is available at http://www.ensemblgenomes.org

Updated elephant and gorilla genomes are now available on the Ensembl Pre! site.

They will be released in full with annotated gene sets in Ensembl 57 (due spring 2010). The new gorilla assembly (gorGor2) includes short-read and capillary sequences. The elephant genome (Loxafr3.0) was also updated, and is at 7x coverage. The 57 release will present new genebuilds for both species.

Ensembl release 57 has been rescheduled for mid to late February 2010.

We had originally planned for release 57 to be this week, but our final quality checks identified a significant error in the unreleased data set. Because of this, we feel that our users would be better served by rescheduling the release to ensure that we provide the best possible data resources for the community.

On behalf of everyone in the project, thank you for your continued support of Ensembl and we wish you all the very best for the holiday season and the new year.

We are pleased to announce the third release of EnsemblGenomes, which includes the first release of two new Ensembl-based portals, Ensembl Plants and Ensembl Fungi.

These complete the span of Ensembl Genomes portals across the taxonomic space, complementing the coverage of vertebrate genomes available through Ensembl.

  • Ensembl Plants has been built in collaboration with Gramene and includes the genomes of six monocots and two dicots. Variation databases are available for four of these species.
  • Ensembl Fungi includes a new build of the Sacchromyces cerevisiae genome using the latest data from SGD, including variation data derived from the Saccharomyces Genome Resequencing Project; and Ensembl databases for Schizosaccharomyces pombe (built in collaboration with GeneDB_Spombe) and eight species of Aspergillus (built in collaboration with the Central Aspergillus Database Repository, CADRE).
  • User upload databases are now operational for Ensembl Protists, Fungi, Plants and Metazoa, allowing users to visualise their own data in the Ensembl environment.

Ensembl Genomes release 3 has been built using Ensembl 55 software. We aim to synchronise with Ensembl with our next release (Ensembl Genomes 4/Ensembl 57), and to stay synchronised thereafter.

The Ensembl project is pleased to announce release 56 of Ensembl (http://e56.ensembl.org/). Highlights of this release are:

Reintroduction of our multi-species views. Alignments (image), formerly alignsliceview, shows pairwise or multiple alignments from the Ensembl Compara database, highlighting any gaps in the alignment.

Multi-species view, formerly known as multicontigview, displays pairwise alignments without gaps; multiple pairwise alignments can be configured to create a multiple alignment display. As well as genes, other types of features such as regulatory features can be displayed in this view, making this a very useful display for comparative genomic analysis.

A new tab has been added in release 56 based on a Regulatory Feature object. This will enable better display some of the data underlying the Ensembl regulatory build. The new pages are accessed from the gene displays by clicking on the ‘Regulation’ link in the left-hand menu and then clicking on a regulatory stable ID in either the image popup menus or the table.

From release 56, users can upload wiggle plot data in WIG and bedGraph formats and view this data on various location-based views. At the moment, only a single style, “wiggle”, is available on Region in Detail, whereas a selection of density plots are available on whole chromosome and karyotype images. In addition, Region in Detail now supports greyscale rendering of BED scores via the useScore parameter in the file, and rendering of features in different colours via the itemRgb parameter and per-feature values.

New data in this release includes gene sets on two new species (Pig and Marmoset) and a new gene set on the existing Rat Rnor3.4 assembly. Also in this release is an updated human gene set which includes all the Havana manual annotation in the merge with the Ensembl automatic annotation set. This set represents the Encode project GENCODE 3b gene set. Also included is a new human variation database based on dbSNP 130 and mapped to assembly GRCh37.

For more information on these and other new features in this release visit:

http://e56.ensembl.org/info/website/news/index.html