What’s new in e!76?
- Updated human assembly to GRCh38 (GENCODE 20)
- Updated mouse gene set (GENCODE M3)
- New BLAST/BLAT
- New Regulation displays
- Improved sequence export
- New species: Amazon molly and Olive baboon
New human assembly – GRCh38
We’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.
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
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
We 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.
We are happy to announce annotation for two new species in this release.
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).
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.
- Updated human GENCODE release 20 and mouse GENCODE release M3 gene sets including manual annotation from Havana
- Imported the latest sequence variants from dbSNP build 140 for chicken, cow, pig and sheep.
- Updated COSMIC version 69
- Updated DGVa data for cow, dog, horse, human, macaque, mouse, pig, zebrafish
- Updated human phenotype from ClinVar and Decipher
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