Ensembl 76 has been released!

What’s new in e!76?

New human assembly – GRCh38

GRCh38We’re excited to release the full annotation of the new human genome assembly (GRCh38). This new assembly includes 24 chromosomes, mitochondrial DNA, 261 alternative reference loci, 127 unplaced scaffolds and 42 unlocalized scaffolds. Our comprehensive GRCh38 resources include updated variation data, results from the new regulatory annotation build, updated comparative genomics data and tissue-specific alignments of Human BodyMap 2.0 data. Full details in our GRCh38 blog series.

There are many reasons to switch to the new human assembly, but if you not able to move just yet, our new archive website http://grch37.ensembl.org provides access to the previous assembly and annotation for those who need it.

New BLAST/BLAT

New BLAST Karyotype view

Release 76 includes our new BLAST/BLAT, which uses the same tools infrastructure as the new web-based VEP that came out in release 75. Highlights of this new version includes the ability to save tickets in a user-friendly table, automatic result retrieval, improved speed and job tracking. We are also now using NCBI-BLAST to enable us to distribute our BLAST code more freely.

New Regulation displays

regulation-display

 

 

 

 

 

 

The display of regulatory regions (sequences that may be involved in gene regulation) has been updated to coincide with the release of the data from the new Ensembl Regulatory build. The major enhancement is a redesigned interface for selecting which evidence types to display and for which cell types, as well as how to display the evidence, for example as peaks or signals.

More details about the new regulation pipeline and displays can be found on the Regulatory Build documentation.

Improved sequence export

new_export_toolWe are embarking on an upgrade of our Export interface to make it more intuitive; the first component to be released is DNA and peptide sequences. To download a sequence, just navigate to a sequence page, click on the “Download sequence” button, select your favourite output format, preview the output file and save it. Note that the “Export data” button has been disabled on pages that use this new interface, to avoid confusion.

New species

We are happy to announce annotation for two new species in this release.

Papio_anubis

The Olive baboon (Papio anubis) assembly, Panu_2.0 (GCA_000264685.1) was produced by the Baylor College of Medicine. This species is used for physiological and behavioural studies as well as comparative genomic studies. BAM files and RNA-seq based gene models are provided through a collaboration between the Nonhuman Primate Reference Transcriptome Resource (nhprtr.org) and the Human Genome Sequencing Center, Baylor College of Medicine (hgsc.bcm.edu).

Amazon molly

The Amazon molly (Poecilia formosa) assembly, Poecilia_formosa-5.1.2 (GCA_000485575.1) was produced by the Aquatic Genome Models Consortium. Amazon molly is used as a model for modern evolutionary biology and carcinogenicity studies, and is extremely easy to breed and rear in captivity. More information on the Amazon molly blog post.

Other news:

A complete list of the changes can be found on the Ensembl website.

Find out more at the Ensembl Release Webinar e76 (Wed, August 20, 2014 4:00 PM – 4.30 PM GMT). Register for free here: http://tinyurl.com/e76-webinar

Want to know more about GRCh38?, Register for free to the Ensembl and GRC Webinar (Wed, September 17, 2014 4:00 PM – 4:30 PM GMT): http://tinyurl.com/GRCh38-webinar

3 thoughts on “Ensembl 76 has been released!

  1. I want to congratulate you guys for the new BLAST interface. I’ve always hated the old one and tBLASTn used to be a nightmare. The new BLAST is a big improvement!

  2. I don’t agree with Michael. While technically it could be an improvment, a lot of things do not work. For example the alignment view comes up with
    ——————– EXCEPTION ——————–
    MSG: Cannot deal with mis-lengthed mappings so far

    The genomic view does not show the blast hit alignment and therefore is useless.

    Please fix these things, otherwise it appears like an alpha release or beta testing.

    Best,

    Sven

    • I’m sorry you’re having problems with the new BLAST – we’d be keen to get them fixed. Could you please email details of your query (input sequence, parameters, you ticket number, what internet browser you’re using etc) to helpdesk [at] ensembl.org and we’ll see if we can diagnose the problem. We haven’t seen the issues you mention so far so we’d be keen to find out what’s causing them.