Yesterday, Ensembl released a new version of the browser and database (version 49). Along with new species, homologue predictions, and new code in our API, there have been changes in how the multiple alignments are done on the whole-genome scale. Have a look at the news for more details.
We are looking forward to release 50! as we are working on some new features. Keep your eye out in August for this next release. A reminder, we will not release another version between now and August, and updates may appear in the Pre! site but not in the main site, for that time.
Please explore features on release 49 such as BLAST which is now configured to align queries against top-level sequences (i.e. chromosomes and scaffolds), and BLAT, a fast alignment program which is now the default selection.
Paralogues are shown in blue in GeneTreeView to help aid your eye.
Upcoming workshops -April
(March workshops are listed in a previous post)
Browser workshops at the VIB Ghent and Leuven (31 Mar – 2 Apr)
Browser workshop (focus: rat) at the ULB Brussels (EURATools) (16 Apr)
Browser workshop at the BCB UCL/Birkbeck (21 Apr)
Module in the EBI roadshow in Poitiers (23, 24 Apr)
API workshop at the Dept. of Genetics, Cambridge (28, 29, 30 Apr)
Keep your eye out for Release 49, which is due on Tuesday 18 March. The delay is due to the scheduled downtime and maintance at the Sanger and EBI this weekend, which has caused some trouble. However, Release 49 will soon be visible to the community!
New features in release 49 will includeBLAST against top-level sequences on all species, updates on theGeneTreeView page that should make things easier to see, and new Ensembl gene sets for Orangutan, Horse and and Takifugu. FlyBase 5.4 will be imported for Fruitfly. For API users, the regulatory features will be moved from the core API to the functional genomics API.
Also, a word of warning to those using our mouse clones under ‘DAS sources’. MICER clones and the bMQ set (129S7/AB2.2 in the ‘DAS Sources’ menu of ContigView). The clones, originally mapped to NCBI M36, are lifted over to the new assembly (NCBIM 37) coordinates. The drawing indicates where the clone lifts over to in the new assembly. However, the pop-up box shows the coordinates of the original mappings. This is indicated in Ensembl by the ‘NCBIM36’ label above the coordinates.
Write our helpdesk if you are confused!
A pig assembly that includes chromosome 5 and 15 has been updated on our Pre! site. See here for further information.
This new release hosts an updated zebrafish assembly (Zv7) along with newly determined gene sets for zebrafish, platypus and chimpanzee.
SequenceAlignView is a new page allowing sequences to be compared across strains (mouse and rat)/individuals (humans). Variations can be displayed in this view. See the sitemap to find the page.
Finally, three new videos are available in the help. See the video tutorials here:
More news is available on our website. Come find out what’s new!
The latest update of the Ensembl Genome Brower and associated databases occurred 13 June, 2007 (release 45). This release was coordinated with the publication of the ENCODE project in the journal Nature. The first stage of this project focused on an in-depth view of 1% of the genome, contributing to a set of regulatory features that has now been incorporated into Ensembl, accessible in ContigView.
BioMart 0.6 has just been released, including an improved layout and response times for result viewing. In addition, the query can be exported in Perl API format
via the new ‘Perl’ button.
Those are the major updates at this time.